Actually Aramike - you could take that "empty" box and open it and say HA - no diamonds - to which a person of faith could point out that the air inside said box contains portions of carbon - the same substance of which diamonds are made. While it may not be VISIBLE to you, diamonds do exist in the box. They are simply not in a form you RECOGNIZE as diamonds.
Spiritually/metaphysically/whatever other term you want to use - the facts are no matter how much you may see - the building blocks are ENERGY. The positive proton, the neutral neutron, and the negative electron. Each atom working in concert with each other - and we still don't understand how or why exactly. But the fact is that if you took an atom with one p/e pair, added another p/e pair - you changed what that atom "is" - and all you really did was modify its mass and electrical charge. *Don't even get me started on Ions and such*
If you see everything as simply energy - the rock is the same as water - just in a different form - or electrical state. Sure this is a VERY basic explanation, but when you get down to the low levels of substance structure - they are made up of the same stuff. Its all energy in motion - just different "charges" or speeds.
So many try to say "Well you can't prove God exists" - or "Well you can't prove He/She/It doesnt", that they lose the beauty of this realm with wasted arguments. I don't have to prove God exists, not to Angus or anyone else. I have enough proof for ME personally, and thats all I need. I see that proof in the things that science can not only NOT explain, but those things that defy every known law of science observed since humanity has been able to record scientific findings. Look at the power of splitting a mere atom - look at the fact that by rights, atoms themselves defy scientific explanation under currently understood physics (since a positive and negative charge would attract and thus cancel each other out - instead of one continually orbiting the other....), etc etc. I need look no further than science to see the wonderful DESIGN of this universe and realize that its complexity is well beyond the human mind to be fully understood. Science is a quest for knowledge - and religion is often the same. They need not be mutually exclusive - though many Athiests feel they should.
The reason Athiests so want to deny a Deity, is because that would make them less than the penultimate being. Pride is a stumbling block for many, but for those that would deny Deity, I would simply point to this world and say, my - how we have so created a paradise by being the "highest being". It is a hard and bitter pill, but if nothing else - humanities failures and we still exist is also a wonderful example of a "higher" hand.
Edit - for those that want to quote science - allow me to remind you of the Law of Conservation of
Matter and Energy - no matter or energy can be created or destroyed - it simply changes form. This law is an amazing statement on the spiritual soul and its relationship to your "living" consciousness - you WILL exist after your physical body dies - so science itself has claimed. One can argue whether or not "you" (being the consciousness in some form) will exist - but there is no way science can prove or disprove that. It simply states that some form of you will exist for all time. People of faith simply expect that form to be one that has a level of awareness in some way. Before you ridicule that, you may want to realize that even things that were deemed "not conscious" years ago (like plants) - have been found to communicate and even reactions that denote intellegence without a known scientific explanation.
See
http://www.theepochtimes.com/n2/content/view/1160/ for an example. Just because science has a theory on something yesterday, or today, or tommorow - does not mean that understanding cannot mature. Do not ridicule just because you cannot fathom it. Your mind is finite. Seek knowledge - and you will find. Be it science, or theology. The wise man seeks to learn, and not merely mock.