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Andrew Beckwith Thanks for your attention, MagnoliaCentipede. To answer your Question A, as I mention in the essay (page 4, 2nd paragraph), our "postulation" of the initial, simplest possible (practically structureless) world system configuration is not a problem as it includes physically and logically inevitable interaction components, while all the observed world structures and dynamical laws are progressively and rigorously derived due to the unreduced interaction analysis (hence its crucial advantages). As to the causal, physical origin of that starting configuration itself, we can only make some reasonable guesses that can hardly be clearly confirmed, since the real world we obtain and can measure doesn't depend on those processes before it was born (we would obviously obtain here an infinite and practically senseless sequence of queries about what was before each past stage).
Question B, about "Gödel’s incompleteness" and other uncertainties: See page 3, 1st paragraph and page 4, 2nd paragraph in the essay. Gödel’s theorem is correct, but physically it is even "too correct", i.e. trivial, because in real-system translation it means that you must know the initial system components to make any definite judgement about further system development, or in other words, that every structure has irreducible links to other structures. This is true, but in reality nothing prevents us from knowing the initial system or interaction process components, especially with the modern technology power. It is not always a trivial, but always feasible task. By contrast, the key point is to correctly obtain interaction products, without any simplification of the process. It is at this point that the essential extension of conventional science results is obtained within the causally complete interaction analysis. Another source of uncertainty that you may have in mind is the dynamically random, unpredictable behavior of real systems, but here again, it's not a problem if we can consistently derive all possible interaction outcomes and their respective probabilities, which is precisely the general result of the same unreduced interaction analysis. We cannot (and I think should not) avoid the probabilistic character of existence, but we must and can know the exact details in all those uncertainties (all real-interaction results and their probabilities). There should be no ad hoc guesses of usual science, in the form of its horribly simplified and abstract "models", but only totally consistent, causally complete analysis of each next interaction level, starting from the provably simplest (and thus inevitable) "primordial" interaction configuration.