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mrstickball said:

- Creation of the universe - how did the matter come into being that created everything we know? Maybe I haven't read up enough, but I haven't found a solid argument concerning how matter even came into being (since that does go against the law of conservation)
- Creation of organic matter - how did matter make the switch from the inorganic into organic? Is this even an observable thing that we can define through empirical study?

Organic matter is nothing special.  We see it all over the universe, it even rains organic compounds on Saturn's moon Titan (methane or CH4, its just one carbon atom and four hydrogen atoms bonded together).  Organic compounds are just the results of chemical reactions, and you do not need a living thing to create organic matter from other atoms.

Creation of the universe, of course, is more 'out there' and I highly doubt anything anybody says will sway your mind.  But anyway...  Think about potential energy.  Consider a rock and put on a table, it has potential energy which is not physical and is nothing more than a definition of its relative position, but when it hits the ground that energy is converted into more physical forms, and you can actually use it to make more mass (energy and mass can be converted to each other, but remember that its a c^2 relationship so a little mass goes a long way).  What about the whole universe?  Everything we know may be a conversion of that non-physical state to something in 'existence.'  And with the universe accelerating away from each other when gravitational energy should be pulling them together, it seems like the universe is correcting itself of its blip and returning to a zero sum energy state.   Or maybe the universe is a combination of positive and negative energy, where the sum of everything is nothing (zero) but positive and negative energy states exists a part from one another.  Whatever the answer is, it makes so much more sense to me to use the same scientific reasoning that has gotten us this far than to try and apply a human-like entity to the equation.