Most of what has been said here will be valid from a strictly mechanistic point of view. The transmutation theory, though, needs a new, holistic paradigm which is based more on the dynamics of energies.
In recent scientific research, a shift is visible from reductionism to holism. It is beyond the scope of this paper to go into this matter. I nevertheless want to take the new paradigm fully into account here in trying to find explanations for the effectiveness of urine therapy. Urine can be considered to contain an exact holographic picture of the body fluids and tissues. The biofeedback of this holographic information by re-ingesting the urine may well inform the energy system in a way which helps restoring a disturbed balance. The medical doctor and urine therapist Abele cautiously discusses the possible effect of urine as holographic feedback: "The question rises as to whether urine could possibly be considered to be a sort of liquid-hologram. Once the body has been made conscious of urine in an unconventional way (such as it being reintroduced into the body by intramuscular injection) the whole organism evaluates it and subsequently updates its own regulating mechanisms (at least in specific cases)."
The theory of transmutation implies that the body is capable, through energetic exchange within the body itself, to transmute certain substances or molecules into other ones. 'Short-circuiting' the system by ingesting one's own secreted body fluids might stimulate the transmutational forces within and challenge the body to transform unusable substances into usable ones without being constantly disturbed by new external input. It could possibly go as deep as to restructure disturbed DNA. This would specifically apply to fasting on urine.
An important aspect here is the theory of structured water. The body consists for the biggest part of water and so does urine. Not all water is the same though. The molecular structure of water can be less or more organized and in the latter case one speaks of structured water. The more it is organized, the better all kind of enzymatic processes can do their job. These enzymatic processes, in their turn, are responsible and necessary for the digestion, absorption and transmutation of all nutrients.
It is scientifically proven how water in biological systems becomes more organized. Water also becomes more organized through exposure to sunlight and through close contact with crystals. The body is both a receptor of sunlight and it contains a high amount of solid and liquid cristallinelike substances. Also body fluids themselves form fluid crystals.
Urine is thus a cristallinelike substance containing a high amount of structured water. This structured water, when taken in again, promotes better enzymatic functioning and it has a higher solubility for minerals. A higher amount of structured water in the body system is correlated with better health and more energy.
The fact that urine is a liquid crystal substance, particularly because of the various salts in it, implies that it contains crystalline vibrations completely in tune with the vibrational condition of the body. Re-ingestion might give the body valuable vibrational information needed for two things. Healthy vibrations will strengthen the already existing, healthy body resonance. 'Diseased' or stress-vibrations will counteract any unhealthy resonance in the body. It is known that disturbing sounds of any sort can be counteracted best by confronting it with the same sounds. The vibratory patterns of the body, both in the bones (solid crystals) and in the tissues and fluids (liquid crystals), play an important role in the process of transmutation. The resonance field of a crystal can make a protein, for example, change its form into one that is more useful for the body, or easier adaptable by it.
Seeing urine as a liquid crystalline like substance containing a high amount of structured water may help understanding its healing qualities on the more subtle levels. This is just one little step in trying to explain the energetical effect of urine therapy on the human organism. This way of thinking should be considered as a kind of scientific, modern 'alchemy'.
There is nothing wrong or scary about this terminology and the way of thinking that goes with it. It is nothing new and at the same time highly modern. It provides a chance to scientifically explain urine therapy in its fullest potential, while at the same time taking into account its rich, spiritually associated, history.
Urine therapy confronts us with a very concrete 'healer within' which works both on a mechanistic and on an energetic level. The latter implies that urine, as a holographic substance, can affect all levels of being, from the physical, through the electromagnetical fields of the emotions and the mind, up to the subtler genetic vibrational information of the soul.