Broken down to basics, much of aquatic chemistry is about charged particles (ions) in water. The ones we care the most about are H+(hydrogen), Na+(sodium), Ca2+(calcium), OH-(hydroxide ion), Cl-(chloride), C(O3)2- (carbonate), H(CO3)- (bicarbonate). The positively charged particles match up with negatively charged particles to make different chemicals. It might sound a little complicated, but don't over think it. It's a little like putting magnetics together...
This chart shows how the different combinations of positive and negative ions give us our basic inorganic additives:
So where do these ions come from? Well, take a look...
1. What's the difference between pH and alkalinity?
pH is short for "power of Hydrogen." It's the concentration of H+ cations in a solution (aka acidity).
Alkalinity is a more complicated beast. In function, it's a buffer. Buffers inhibits sudden changes in pH over a certain range. The ability of the buffer to prevent sudden changes in pH is called a "buffer capacity." As we usually use the term in the hobby, alkalinity is the "buffer capacity" of our water. Bicarbonate and carbonate are the major contributors to alkalinity. They're not the only contributors, but in our tanks, they're by far the most important. (The contribution of borate is an interesting topic discussed briefly at the end of this page.)
2. Is aragonite a good Ca/alkalinity supplement?
No. The answer as to why is a bit complicated. But basically, there's already so much Ca and CO3 in the water already, that additional CaCO3 isn't going to dissolve unless you put it in more acidic conditions. The pH of your tank water should never be low enough to dissolve appreciable amounts of aragonite.
3. What do the alkalinity tests actually test for?
Most don't test for any one compound. Most of them are titration kits that give you an idea of buffer capacity by finding how much acid it takes to break the bicarbonate/carbonate buffer (the point at which the buffer can no longer inhibit the change in pH).
5. Where do dissolved silicates come from?
They can come from a lot of different sources, but mostly from unfiltered tap water. Contrary to what might seem intuitive, dissolved silicates do not come from silica sand.
6. What about Boron?
Boron exists in sea water as Boric Acid (B(OH)4)- and Borate, B(OH)3. Which, together, are a weak acid and its conjugate base. Y'all know what that means right? It's a BUFFER! And just like with the bicarbonate/carbonate duo, it affects alkalinity. Now, this gets really geeky reefers all excited because artificial salt mixes are often much higher in Borate/Boric Acid than natural sea water. So when they measure their alkalinity with a test kit (which almost certainly only measures alkalinity due to bicarbonate/carbonate), they might not be getting a very accurate measure of the tank's true buffer capacity.

