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Benjamin,
Your paper suggests that many assumptions are patched together in an effort to make them fit a preconceived model, even though many of the assumptions are widely doubted. It is comparable to the elephant problem, each observer description comes from someone that is standing too close to the object under investigation and each observer has a limited range of observation. Then the observers get together and try to put the observations together to fit a preconceived model. A problem arises when the observers do not recognize their preconceived model may be completely in error, and as a result they are filling in the unknown spaces with assumptions that they do not all agree on, but they tolerate the assumptions because they do not want any empty spaces.
Quote from your essay: "The first few assumptions I reject are that spacetime is a manifold, that systems evolves with respect to an independent time parameter, and that the universe has a static background structure."
I can agree with rejecting the first assumption. The IEEE paper I cite in my topic, 1294, titled, "A methodology to define physical constants using mathematical constants" contains a mathematical relationship where time is a dependent function. Basically, TIME, as an event duration, is a function of the existence of energy. Sounds radical, but it is completely logical mathematically, without the presence of the parameters that define energy there is no need for TIME.
I notice you do not reject the contemporary assumption on the theory of gravity. If that assumption is wrong then all the assumptions built around it are suspect. I have a paper that I am subjecting to open peer review at the moment that describes the EM field structure that creates an attractant only force. I didn't feel it has had sufficient outside review for this contest, but it is coming together. I added two references in response to one of my reviewers comments, [6] "Electrifying Gravity", and [7] "Newton's Gravitation Constant G as a Quantum Coupling Constant".
I was unaware of the existence of the two papers I just cited when I originally prepared my paper, I have been working on it for several years. I found the references during a search for the term "quantum coupling". Those two papers should be required reading for those that are attempting to build a model of the universe.