Prim=atom? Ruh?

From the video that we observed in class, I can't stop thinking about how he classifies a prim in the game to an atom in the real life. To me, I can't fathom that comparison however anyone tells me. Something we can't see or feel that makes up the world compared to something we can easily shape, change color, twist, and make our own. From what I just said, it sounds like we get to play God, not until we go to scripting where we can actually make this object we create into something that can reply from touch or time ( all depends on the creator/scripter).
But, think back to what else he said, he mentioned he was supposed to be a physics man, and yet this breaks all laws of physics we can attempt in this world and yet he says this is a "sufficient" second world. I guess from the eyes of someone who knows coding languages, designing programs, and real world chemistry,physics, and then try to combine them is illogical.
I also understand that it's not our world and I should suspend my disbelief while in the game but this is just a copy of the what my disbelief is! I can't just say this is realistic and make up my own version of realistic like he says, it the definition and true form of Chaos, where so many mind come together and are not limited. So instead of challenging what he said about atoms and prims being the same, I think I more challenge his thought of Second Life being a virtual equivalent of our world. Because it's impossible to have stuff in Second Life in the real world until we realize two more dimensions and have the power to create stuff that can even hope to rival what the human mind can think of.