Energy is a fictional entity posited to explain phenomenon we observe or quantify. Effects of heat, light, magenetism, movement and so on are explained through the positing of various forms of energy as causal. Energy itself however is never perceived in any of these. It remains unknown in terms of its composition, components or nature.
Energy ('mass is energy') and force (as with magnetic or gravitational forces) concepts are almost magical in nature, stuff used in physics, calculated, predicted, without really being understood, a vague grasp as opposed to a deep understanding. Hume is a good reference here as we only perceive effects rather than causes and there is no real way to identify causes except circularly through referring to effects. We can treat the term energy as a fictional entity and continue to use it as a useful concept without making ontological claims about it.
Such questions have always accompanied physics having never been settled. The Positivist compromise defines scientific concepts functionally as whatever works. If the underlying mathematics is consistent, the predictions correct and experiments repeatable the fiction can stand until it is falsified, refined or replaced. Occam's Razor, essential for theory selection, cannot be proven or founded in reality. Thus the success of physics depends on ignoring such questions. Physics says "how" but never ultimately "why" or "what". The classic example is quantum theory, which works perfectly in engineering and is mathematically precise, yet know one knows what on earth we are talking about. We cannot even imagine the "reality" in any experiential terms. To ontology, physics says, in effect: Don't ask, don't tell.
The working physicist leaves ontology at the doorstep, many physicists, usually the greatest ones, have thought and written much about these matters. You might take a look at Heisenberg's "Physics and Philosophy" or Paul Davies "The Matter Myth" or works by Bohr. When "off duty" these minds cannot help it. They are nagged by your very questions and need to get at the "reality" behind them.
Richard Feynman in The Feynman Lectures explains this well through considering the idea of energy:
What is Energy
In this chapter, we begin our more detailed study of the different aspects of physics, having finished our description of things in general. To illustrate the ideas and the kind of reasoning that might be used in theoretical physics, we shall now examine one of the most basic laws of physics, the conservation of energy.
There is a fact, or if you wish, a law, governing all natural phenomena that are known to date. There is no known exception to this law-it is exact so far as we know. The law is called the conservation of energy. It states that there is a certain quantity, which we call energy, that does not change in the manifold changes which nature undergoes. That is a most abstract idea, because it is a mathematical principle; it says that there is a numerical quantity which does not change when something happens. It is not a description of a mechanism, or any- thing concrete; it is just a strange fact that we can calculate some number and when we finish watching nature go through her tricks and calculate the number again, it is the same. (Something like the bishop on a red square and after a number of moves-details unknown-it is still on some red square. It is a law of this nature.)
Since it is an abstract idea, we shall illustrate the meaning of it by an analogy. Imagine a child, perhaps "Dennis the Menace," who has blocks which are absolutely indestructible and cannot be divided into pieces. Each is the same as the other. Let us suppose that he has 28 blocks. His mother puts him with his 28 blocks into a room at the beginning of the day. At the end of the day, being curious, she counts the blocks very carefully and discovers a phenomenal law- no matter what he does with the blocks, there are always 28 remaining! This continues for a number of days, until one day there are only 27 blocks, but a little investigating shows that there is one under the rug-she must look everywhere to be sure that the number of blocks has not changed. One day, however, the number appears to change-there are only 26 blocks. Careful investigation in- dicates that the window was open and upon looking outside, the other two blocks are found. Another day, careful count indicates that there are 30 blocks! This causes considerable consternation, until it is realized that Bruce came to visit, bringing his blocks with him and he left a few at Dennis' house. After she has disposed of the extra blocks, she closes the window, does not let Bruce in and then everything is going along all right, until one time she counts and finds only 25 blocks. However, there is a box in the room, a toy box and the mother goes to open the toy box, but the boy says "No, do not open my toy box," and screams. Mother is not allowed to open the toy box. Being extremely curious and somewhat ingenious, she invents a scheme! She knows that a block weighs three ounces, so she weighs the box at a time when she sees 28 blocks and it weighs 16 ounces. The next time she wishes to check, she weighs the box again, subtracts sixteen ounces and divides by three. She discovers the following: Equation 4.1 There then appear to be some new deviations, but careful study indicates that the dirty water in the bathtub is changing its level. The child is throwing blocks into the water and she cannot see them because it is so dirty, but she can find out how many blocks are in the water by adding another term to her formula. Since the original height of the water was 6 inches and each block raises the water a quarter of an inch, this new formula would be: Equation 4.2 In the gradual increase in the complexity of her world, she finds a whole series of terms representing ways of calculating how many blocks are in places where she is not allowed to look. As a result, she finds a complex formula, a quantity which has to be computed, which always stays the same in her situation.
What is the analogy of this to the conservation of energy? The most re- markable aspect that must be abstracted from this picture is that there are no blocks. Take away the first terms in (4.1) and (4.2) and we find ourselves calculating more or less abstract things. The analogy has the following points. First, when we are calculating the energy, sometimes some of it leaves the system and goes away, or sometimes some comes in. In order to verify the conservation of energy, we must be careful that we have not put any in or taken any out. Second, the energy has a large number of different forms and there is a formula for each one. These are: gravitational energy, kinetic energy, heat energy, elastic energy, electrical energy, chemical energy, radiant energy, nuclear energy, mass energy. If we total up the formulas for each of these contributions, it will not change except for energy going in and out.
It is important to realize that in physics today, we have no knowledge of what energy is. We do not have a picture that energy comes in little blobs of a definite amount. It is not that way. However, there are formulas for calculating some numerical quantity and when we add it all together it gives "28"'-always the same number. It is an abstract thing in that it does not tell us the mechanism or the reasons for the various formulas.
Source: The Feynman Lectures on Physics, Vol 1, Chapter 4: Conservation of Energy
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