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Last night I attended my first "internal arts" practice. My understanding in brief synopsis of how Itten Dojo got into this practice is this: Ellis Amdur has been studying, and to a certain extent, deconstructing O Sensei's aikido for a number of years. A few years ago, the folks at Itten Dojo started working with Ellis to explore and implement Ellis's ideas on aikido.
In recent years, Ellis has determined that a lot of O Sensei's power came from an understanding of "internal martial arts," or "internal training." I don't really know much about internal training, but I've seen the results. The principles work and make for powerful movements and techniques. Ellis connected Itten Dojo with Mike Sigman, who has made internal training a major focus, and gives workshops on it. This interview with him is interesting: http://www.iay.org.uk/internal-strength/related/interview.htm
From what I can tell, a lot of what we're doing is similar (or even identical) to the emphasis on ki development like Koichi Tohei did. I'm not sure about the differences yet. I really don't know enough about what I'm learning to be able to speak with any authority, but the general aim of the training seems to be like ki as it is taught in traditional aikido.
There are differences, though. I feel them when I train. One of the primary difference seems to be a very detailed and mindful study of internal training principles at Itten Dojo. For me, this is the difference between being aware of something and participating in detailed study and repetition. Like the difference between know what a musical chord is, and practicing arpeggios until they become second nature.