Since this is in the backroom, I'll make a few comments but try to keep them brief:
On the "what is a closed system" issue it should be remembered that space and time (including real or absolute time) are not boundaryless and therefore there is no truly open system in physical reality. Other conceptualizations of “open” systems make the contrary presupposition but are actually, physically closed (geometrically speaking because of space/time).
On the transformation of energy and matter, the very definition of matter v mass v energy causes confusion because each use the other in their explanation.
Take relativistic mass for instance, the observed mass increases as an object approaches the speed of light. The term “energy” is often used in lieu of relativistic mass.
And E=MC2 transforms to M=E/C2.
Yet massless particles (such as light or photons) do not have a rest frame and thus are described as E=pc (p=momentum and c=speed of light). No time elapses for the null path. Conversely, for massive objects the formula is E2/c2=m2/c2+p2.
Further, when matter and anti-matter collide they are mutually annihilated, and energy is released in a burst of radiation.
And matter is also created by energy in pairs, as in the case where two or more photons interact so to create a new fermion/antifermion pair.
Consider also that the critical density of the universe is comprised of 5% ordinary matter, 25% dark matter and 70% dark energy.
After all, Einstein’s dream was to transmute the base wood of matter into the pure marble of geometry.
Geometry is at the root.
The really "big" picture! The thought occurred to me that your observation goes straight to Liebniz's two great questions: Why is there something, why not nothing? And why are things the way they are, and not some other way?
It seems to me neither question can be answered on a theoretical basis that gives a major role to "randomness" (or "boundarylessness") in nature. Whatever "randomness" is. I'm beginning to think in many cases maybe it's just the stuff we humans can't otherwise account for. We are "conditioned," it seems, or "naturally selected," whatever, to be strongly visually oriented. And this basically means that the stuff we "see" is only that which lies in the 4D spacetime band, which classical Newtonian physics so ably describes.
In my reading lately I came upon a term to describe this 4D spacetime band: the "mesocosmos," closely correlated with Newtonian physics. In this model relativity theory deals with the "macrocosmos"; QM with the "microcosmos." All constitute the reality that we human beings experience and observe, all the details of which are not consciously experienced by us.
Jeepers, I hope I can find that source!
Anyhoot, there has to be a "beginning." So that part, at least, isn't "random." And if there's a beginning, we cannot dispense with the possibility that the beginning was made to achieve a purpose. And so we can begin to speak of "progress." Whatever that means to the person using that word.
Just a little wool-gathering there, dear Alamo-Girl! Thank you for your splendid and most valuable post!