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The point that I think that you may be missing is that the right frequencies are what is needed to do the job properly.
In other words, having the right frequency applied is more important than the method of applying it.
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No the right frequency/ies is not enough, there must also be a high enough intensity to break the molecules.
You cannot break a glass with a low intensity, you need a high enough intensity.
See http://www.youtube.com/watch?v=qReUmruqUoc
This is why the method of delivery can make a difference, the human body has more resistance to some phenomenons than others. For example it may be easier to reach a specific area in the body with an electromagnetic field or with a magnetic field than with a current. This video gave me an idea, maybe sound waves can reach the inside of the body with a high enough intensity.