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While some diseases are of short duration and mainly affect one part of the body, others progress to affect additional parts of the body and can eventually engulf the entire organism. As described by Rob Svoboda: "Weakness of the digestive fire is the root cause of all diseases, vata is the chief cause of the development of all diseases, and ama is the principal nourisher of disease." The primary stages of disease are depicted as accumulation, aggravation, and overflow.

Accumulation: As a result of exposure to various disease-causing factors, one or more of the doshas accumulates in its seat: kapha in the stomach, pitta in the small intestine, and vata in the colon. Each produces its own characteristic symptoms, for example: kapha creates lethargy, heaviness of the limbs, pallor, bloating, and loss of appetite with weakened digestion; pitta produces burning sensations, increased body heat, a bitter taste in the mouth, yellowness of the skin, acidity of the stomach, and increased anger; vata causes weakness and dryness of the body, desire for warmth and hot articles, stiffness and fullness of the abdomen, flatulence and/or constipation, disturbed sleep, and increased fear. The disease is relatively easy to resolve when the imbalance is primarily one of accumulation.

Aggravation: In this stage, for which the Sanskrit term literally means rage, the doshas continue to increase and put pressure on their reservoirs, intensifying the symptoms they have produced. It is still fairly easy to remove the doshas (as faults) even at this stage, but while treating them, their reservoir organs, which have been stressed by the ire of the corresponding doshas, need also to be strengthened. The doshas do not always accumulate before they become enraged; if the causes are strong enough, aggravation of doshas at their normal levels may occur directly.

Overflow: If aggravation is permitted to proceed unchecked, the doshas escape their original seats, wandering about the body like vagabonds, searching for a place to camp. All the symptoms that already existed from aggravation now worsen. At this point, kapha may produce vomiting, pitta may produce burning diarrhea, and vata may produce colicky pain in the colon and painful defecation, with the liberation of copious quantities of gas. Overflow of pitta or kapha can occur without previous accumulation or aggravation in their reservoir organs if either or both of those doshas are displaced by the force of a strongly aggravated vata. This "wind" may be directly disturbed by exposure to strong imbalancing causes, such as excessive desire, sleeplessness, excessive talking and activity (especially on an empty stomach), sudden vomiting or diarrhea (particularly if self-induced), intense joy or sadness, and the restraint of any of the natural reflex urges.

The fourth stage (purvarupa) is the initial manifestation of symptoms that result from accumulation of the doshas at susceptible sites. The fifth stage (rupa) is when the disease has become readily apparent: the sites of secondary accumulation of the doshas have been substantially disturbed; there are local structural changes. The sixth stage is when the disease erupts from the body. At that point, symptoms might include obvious inflammation, enlarged glands, abscesses, skin eruptions, fever, diarrhea, leukorrhea, etc. That is, there are indications that the body is filled, and material is either stuck (as in a swelling), erupting, or draining out. At the same time, complications of the disease, manifesting now at additional sites, will occur.

The therapies at each of the stages as the disease progresses must become more specific, more potent, and more frequently applied. It is best to catch the disorder early, when dietary adjustments and a few days of using simple herb formulas may be sufficient; perhaps massage will be applied once or twice, and some cleansing procedures might be followed.