These are very good questions, and you are not alone in asking them. The ancient Greeks, specifically the presocratics, often thought and argued these questions. There were three main guys who came up with ideas of what the universe was made of, one of their answers came very close to the same question you asked in section one. The presocratics were mainly obsessed with finding the ARCHE (ark-AY) of everything, which meaning the ruling principle (the stuff that made up everything else).
Thales of Miletus believed that the arche was water. He believed that everything, when it died, eventually liquified. Today we know this not to be true, since we can identify the smaller parts of water. The main argument of this would be if everything is made of water, then why doesn't everything have the properties of water?
Anaximander of Miletus believed that the arche was the APEIRON, meaning the limitless, or the unbounded. He believed that the stuff that made up everything was:
1) Limitless and unbounded with respect to size (could be infinitely small or infinitely large).
2) Limitless and unbounded with respect to time (has no beginning, and no end. Exists of itself)
3) Limitless and unbounded with respect to material properties (Could have the property of anything existant.)
4) In motion eternally (We classify motion by change.)
So the stuff that Anaximander believed made up everything else was infinite in number, properties, age, and change. Even though this theory seems simple and unscientific there is little that can refute it because it is all encompassing (not to mention a little vague). Suggesting that water is made up by the same material as fire seems a little odd, but when one allows that the APEIRON makes water to exist with water's properties when it is water and fire to exist with fire's properties when it is fire the theory can fit. For example, Coal and Diamonds are made up of the same molecular composition, but arranged differently, therefore they have different properties.
Only a few fragments of Anaximander's work still exist, but we do have a quote from another author, Simplicius, that still exists.
"The things that are perish into the things out of which they come to be, according to necessity, for they pay penalty and retribution to each other for their injustice in accordance with the ordering of time, as he says in rather poetical language."
I feel that no matter how close we get to truely understanding what the arche is, we will never really find it because, when size is a issue can't something always be "smaller"? And can't that smaller thing be larger compared to something else? We have not come very far in over 2000 years of philosophy and science when we consider this question of the arche.
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But I will seek the meadows by the shore: There will I wash and Purge these stains, if so I may appease Athena's wrath. Then will I find some lonely place, where I may hide this sword, beyond all others cursed, buried where none may see it, deep in earth.
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