Hmmmmm. Those are toughies. These are my thoughts on this.
Crystals not only have their own energy source (Channelled from The Source, no doubt.) but they also have personalities. A lot of sites and books that talk about what a crystal is supposed to mean are guidlines. A big thing about Crystal work, is you have to listen to the crystal. You have to make a connection with it, and listen to what it has to say. It will tell you what it will do for you, it will tell you what it prefers (sunlight or moonlight, lying out in the open or in cloth, being worn or not. Male or female, how it likes to be held. ) If you are, in a way their best friend (you get to know them, meditate with them, place them so you are near them a lot) then they will help you for as long as you need it. they will do what They, individually, can do for you without asking. Also, a lot of properties have been assigned by very intuitive people, and they are told by spirit and crystal what properties they have.
Crystals just are. A lot of attributes are, lets say, Traditional. Traditional as in first peoples who found them and assigned properties to them. Religious belief, meanings of colour, and basically what the crystal said to them. from there it was passed on and more was added. I doubt where they were discovered has any effect, but many believe that they hold the wisdom and stories of the soil that held them. I could agree, since the earth is made up of so many energies, that crystals would absorb what She knows.
I guess its safe to say that the colour and structure (and stuff its made of) effects the frequency, so it's more suited to one property than the other.
I think the last bit does belong here, because im not sure it belongs anywhere else.

I don't think that scientific understanding will effect it much, except in the way of faith. if you BELIEVE that knowing biology, the physics of energy and about the formation/structure of the crystal makes you able to use them more efficiently, then it will, simply because you believe. Its amazing what belief will do.
So someone who doesnt know much about biology, formation/structure of the crystal, or the physics of energy will still have the same healing abilities as one who is very knowledgable about it. (Unless the knowledgable one shoots down the other person, making them think their abilities are lower.

Again, it all has to do with FAITH.)
Hope i was helpful and didnt confuse you. I tend to ramble a bit.
Much Love,
~effie
PS. I think i remember you saying you were interested in EC, and for anyone else interested in EC, sites and books talking about properties are good guidlines for EC's. EC is really just a concentration of energy formed by intention to mimic healing properties of crystals.
