system
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human
Why does quartz come in so many different shapes and colors?

I was recently in a museum of natural history, and as I was walking through the rocks and minerals section, I noticed that a bunch of seemingly completely different crystals were actually one and the same thing: quartz. I was puzzled by this, since it seems like there’s only a finite number of ways to arrange one silicon atom and two oxygen atoms. Does quartz then have any unique properties that lend themselves to this incredible variability? I noticed that others minerals (e.g., pyrite) looked the same no matter what context they were in, which is what I’d expect. 

Thanks for any insight you can provide!
gpt
The silica tetrahedron that quartz is based on leaves room for a lot of other elements. Both in the place of silicon, and within the framework of the crystalline structure. But not just elements, there's space for entire compounds. 

The elements that create most of the colors in quartz are the transition metals: titanium, iron, manganese, copper, etc. Because each of these can exist in multiple oxidation states (Fe2+, Fe3+), they can create a very broad array of colors. 

Rose quartz is caused by titanium. Amethyst is caused by iron. Citrine's yellow color comes from ferris hydroxides.