I recommend you read the Embryonic Breathing book. It is explained in detail from both Eastern and Western perspective, from beginning to enlightenment.
http://ymaa.com/publishing/books/qigong/qigong_meditation_embryonic_breathingI'll try to summarize. I've been studying with Master Yang for 12 years now.
Internal alchemy is referred to in many cultures around the world, including most ancient civilizations. In Buddhism, Daoism, and qigong, it refers to the process of increasing your body's energy, and clearing the mind, allowing the body's energy to be directed inward for meditation.
It involves conserving and stimulating your hormone production, which was referred to in ancient documents as 'essence'. Through the metabolic process, and deep breathing and accumulation of ions, the body's cells are energized. Hormones act as a catalyst in the body to expedite the metabolic process, releasing more energy, which is then conserved. In addition, the mind is calmed, the sympathetic nervous system relaxes, the immune response improves, and this healthier state of mind allows for healthier gene expression, with lasting benefits, even overcoming genetic predispositions to disease.This is studied in the emerging Western medical fields of Epigenetics and Psychoneuroimunology.
With the practice of embryonic breathing meditation, you learn to calm the emotions, focus your energy in the brain inward to the limbic system, and then lead it down into the abdomen, which is the location of the second brain in the human body, known as the enteric nervous system.
Sit up straight. Inhale, draw the abdominal muscles in and up gently, hold your mind in the center of the abdomen. Exhale, relax.
Then begins a long process of refining your body's chemistry, conditioning the muscles, tendons, bones to circulate a higher capacity of energy, working through muscular issues and energetic blockages, and experiencing extended durations of samhadi, in which the consciousness becomes one-pointed. You are present in the moment and your energy is drawn to the centerline of the body, and over time, your energy is led upward into the center of the brain. Because brain cells consume a tremendous amount of oxygen and energy, it is necessary to cease all thoughts and meditate, allowing your energy to settle into the pituitary and pineal glands. (Observing the breath is often recommended for capturing the mind.) The brain focuses and relaxes into a slower more intensified brainwave frequency. Eventually, the mind's intensified energy from the area of the pineal gland is focused forward to the third eye, through the spiritual valley, the resonant chamber between the two hemispheres of the brain. The bone in the third eye area becomes energized to threshold voltage and opens. This a part of the physiological process of enlightenment. And our energetic and spiritual cultivation proceeds after that as well. Of course, the mental aspect of the practice, as described so well in Buddhist sutras, is the most difficult to master.
Some schools, especially in modern times, focus on the mind alone and neglect the body. Bodhidharma arrived at Shaolin and found the monks to be weak physically, and mentally deluded. There he brought Buddhism to China deeply, and though others taught before him, he is considered the first Buddhist patriarch in China. At Shaolin he meditated for nine years and then emerged with two written documents about the body's energetic system and how to train for enlightenment with qigong. This written theory is considered the start of 'internal' martial art styles in China, in which increased energy is used for self defense. The ancient understanding of the body was learned over hundreds of years through feeling during meditation, and has been well documented in the journals of monks from various traditions. Bodhidharma preserved the technical theory of Buddhist practice, and transmitted it to China.
To get a clear view of who Da Mo was, I recommend this great book, which translates the actual verbal teaching of Da Mo while at Shaolin. He is very tough, and it is as clear and eye-opening today as it was then:
http://www.amazon.com/Zen-Teaching-Bodh ... 0865473994 All the books by Red Pine are excellent.
The ancient theory of the body's energetic circulation relates clearly to modern Western medical research. Our bones are semiconductors, and piezoelectric, meaning they generate energy when stressed. The fascial planes and intersections in the body cause pools of energy to form, matching exactly the location of the acupuncture points, as well as the Indian chakras, also known in qigong as the seven pairs of matching gates.
Dr. Yang has a Ph.D in physics and is able to explain energy in modern scientific terms in a clear, no nonsense way. We are fortunate at this point in history to have a clear map for the first time, easily cross-referenced with Buddhist sutras, National Institute of Health studies, and various recent accounts of modern-day masters with great longevity, vitality, and even enlightenment.
And stuff.