Why is all matter in the universe, not found at its lowest state of potential energy? Preface: it may be of interest that I am a second year Biology student, with no experience in studying Physics and a very basic understanding of Mathematics. However, I have some experience studying introductory Chemistry. Where I make incorrect assumptions and show an obvious lack of knowledge (e.g., using terms incorrectly), feel free to correct me, on a scientific basis.

Onto my question, why is all matter* (anything that takes up space and has mass) in the universe, not found at its lowest state of potential energy? Now, I warn you, there will be many related sub-questions throughout this post.
In the past, people have answered this question by saying that matter that is already at a higher potential energy state can be trapped there due to 'barriers', analogous (I imagine) to a table carrying an object, preventing it from falling. Firstly, this does not answer my question, which is more concerned with why the object got on the table in the first place, more on this is below.
Secondly, the next sub-questions follow: how does some matter prevent other matter from reaching a lower potential energy state? What distinguished the matter being prevented from reaching a lower potential energy state, from the matter preventing it? Side note: it would be nice to know the formal name for these 'barriers' or 'preventative matter'. Does the matter preventing the other matter from reaching a lower potential energy state, exchange energy with the matter it is 'blocking'?
My thinking: theoretically, if some matter loses energy (it will go to a lower potential energy state), other matter will absorb this energy (it will go to a higher potential energy state). Which makes me wonder, why does/did matter exchange energy whatsoever? Such energy transfer, would lead to some matter going to a higher potential energy state and other matter going to a lower potential energy state? Why is all the energy in the universe not evenly dispersed between matter? Why does energy transfer or more generally, energy exist? What is 'energy'?
How can some matter decide to exert energy? For example, when an organism decides to lift its limb against gravity.
As you can imagine, these questions cause me immense confusion in the context of understanding Biological phenomena at any scale, including at the scales of Chemistry and Physics (especially since these subject are essentially one whole, as the distinctions between these subjects are arbitrary). My confusion is exacerbated by the alleged fact that Biological matter is found at a higher potential energy state compared to 'non-living' matter, why is this the case?
My following 'philosophical thoughts' (if you can call them that), it is probably more useful to see them as an insight into my way of thinking, add to my own confusion (these questions may arise from my critical lack of understanding of the fundamental concepts of knowledge, science and physics) or maybe they highlight gaps in human understanding (which I do not claim or believe they do).
Philosophy: I must admit that I do not what mass is exactly (relevant because my question is to do with matter*), because I have not studied physics and partly because I believe, like all definitions, words and concepts (abstract ideas), 'mass' is arbitrary (here I define arbitrary as: anything resulting from personal choice). It seems logical to me, that the distinctions humans and all other living organisms make between any two things (by using the word 'things', I am implying distinction exists outside of consciousness), must be a product of personal choice. In other words, we (i.e., humans and other living organisms. Side note: this is itself a distinction that does not necessarily exist outside of our consciousness, I for one, personally, do not see a reasonable distinction between living organisms) make distinctions between 'things', which we arbitrarily define (perhaps for an evolutionarily advantageous reason), the 'universe' excluding living organisms, does not. However, under my 'logical' reasoning, if the distinction between 'life' and 'non-life' is also arbitrary, (we can be seen as a part of the universe, or indifferent from the universe, either way, our consciousness is a part of the universe, or is the universe, and thus, our concepts, definitions and words do exist in the universe, as do the concepts, definitions and words of other individuals and living organisms) then all of these possible arbitrary distinctions exist in the universe.
Anyway, I am getting a headache and you probably are too, I am now questioning whether there are 'real' or physical distinctions between matter. All of this confusion arises because all humans, no, probably just me, clearly do not understand 'reality'.
 A: 
why is all matter* (anything that takes up space and has mass) in the universe, not found at its lowest state of potential energy?

Consider the Moon orbiting the Earth. The lowest state of gravitational potential energy would be if the Moon fell down on the Earth and become a part of it.
As Moon orbits the Earth, its potential energy varies slightly - it decreases when the Moon is approaching Earth, and it increases when the Moon is leaving the Earth. But it is an oscillatory process, potential energy never goes down and stay there. Moon does not fall down.
Why does the Moon not fall down on the Earth? It is falling in some parts of the orbit, but because it is also moving sideways, it can't easily hit the Earth. When it is approaching the Earth and losing potential energy, it gets higher orbital speed (as the lost potential energy transforms into additional kinetic energy of the Moon). This higher orbital speed affects later stages of the orbital motion: it makes it impossible at later stage of the orbit to continue approaching Earth. There will be a point where the approach stops and the speed is becoming great enough for the Moon to start leaving the Earth again. Orbits in central gravity field are stable, and gravity force alone can't get the body down from the orbit. This is a special property of gravity force that other forces need not have. We could imagine that gravity or other force was so strong it would pull everything towards the center and no stable orbits would be possible. But natural forces are usually not like that, and that is physical law.
Back in the Moon example, it would be different if there was another force that would slow down the Moon and make it lose kinetic energy and prevent its retransformation into potential energy. This happens to artifical satellites on a low orbit - the atmosphere provides friction force that modifies the motion into a decaying orbit. It steals energy from the satellite, the satellite then falls down deeper and never gets to the original height, and eventually it will fall so deep that it may burn up or fall down on the ground.
A: 
Why is all matter in the universe, not found at its lowest state of potential energy?

Because potential energy and kinetic energy are fighting each other and for potential energy to win, kinetic energy must be zero. This, however, is possible only at zero temperature. At all other temperatures there is always some (or a lot of) kinetic energy. As long as a system has kinetic energy (think of a pendulum) it will never rest at the point of minimum potential energy. To freeze the entire universe we need a bath somewhere outside the universe to dump this kinetic energy.
