Several martial arts bloggers have weighed in on this topic lately in various forums. I wanted to throw my understanding of ki out there because if you're going to try to understand ai-ki-do then you need to understand what is supposedly at the center of it. I also recently re-published an article somewhat related to ki and I wanted to clarify that concept a little if I can.
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Ki is simply another word for Energy. I like the current wikipedia definition of energy:
In physics and other sciences, energy (from the Greek ενεργός, energos, "active, working")[1] is a scalar physical quantity that is a property of objects and systems which is conserved by nature. Several different forms, such as kinetic, potential, thermal, electromagnetic, chemical, nuclear, and mass have been defined to explain all known natural phenomena.
Notice, energy is a property of things - it is not a thing itself. Ki is the same. Just because things (like people) have ki (energy) does not mean that ki is a supernatural spirit that lives in the belly of people and circulates through meridians and can be made to perform magic tricks, etc... People, just like every other physical thing, have energy.
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Energy is the ability to do work (i.e. to make things move)
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So, how does this relate to ki in the context of aikido? If ki is energy (the ability to make things move) then aikido is an art (or skillful method) for getting into harmony with energy - specifically the ability of an attacker to move us. In aikido we talk a lot about kito, which is the theory that energy rises and falls and changes form all the time. We also talk about kimusubi, which literally means "binding ki" but which translates more practically to the idea of synchronizing the changes in your energy to the changes in your opponent's energy to obtain an objective (i.e. not getting hurt).
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One last point... As scientists, we have a pretty vast experience in watching energy change forms. We become accustomed to what energy transformation looks like. If you see something in aikido (or another martial art) that looks like magic. If it looks like energy changing form in some alien way (i.e. action at a distance) , something else is happening (like uke jumping).
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Harmonious energy transformation (i.e. aikido) works via natural processes and tends to look like it works through natural processes. Occasionally these natural processes are extremely efficient and skillful, but they are not spiritual ki magic.