Why thermal energy is treated differently than other kind of energies?

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If “E=mc²”, where “E” is energy, if “W=delta-E”, if a change in gravitational potential energy produces work transforming into kinetic energy, if a change in kinetic energy produces work, if a difference in electrical potential is converted into a change in energy or work, if, in the end, different “E” (i.e., energies) is always a ‘theoretical’ (i.e., didactic, because energy is energy) transition of a fundamental manifestation — energy —, if every action produces a reaction (Newton's third law), then why is thermal energy the only different one? Why can thermal energy be used in science to generate work (e.g., combustion of petroleum derivatives), but cannot be used to explain the change in kinetic energy and the work done by the boiling motion of water inside my pan? Why, only in what is tangible to any human being in the world, does energy transformation cease to be a vector force like all the others and become a mathematical tautology?
 
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I have no idea how to parse this run-on sentence. What is your question?
if every action produces a reaction (Newton's third law)
That's a statement about forces, not energy.
Then why is thermal energy the only different one?
Different from what?
The difference in unordered kinetic energy of water molcules is the gain in thermal energy if you heat water.

E = mc^2 is the energy of an object at rest.
 

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