Dear Sir,
Your reference to the questions about the nature of mass is important and timely. QM and its extensions are wandering to solve many problems, but without any direction. The various competing theories and interpretations impede progress. One such area is mass, "evolving from material content in a body to the assembly of stable elementary particles, representing "pure energy" in some form (m=E/c^2)". If you look at our ancient concepts, they insisted on three complimentary characteristics of matter, energy and perception called Tama, Raja and Sattwa, which coexist everywhere and cannot be separated fully. The determining character is dominance of one over the others. Thus, energy confined as mass, which is evident from your notation: m=E/c^2. Here E is confined in an area represented by c^2 (otherwise m will continue to increase per every second, which is contrary to observation) to provide a density gradient, which is mass in that context. Similarly, when mass is moved and inertia overcome, it is called energy. Everything in the universe is in a state of perpetual transition. This transition is perceived as mass or energy based on their degree of dominance.
In a previous paper in this forum (REASONABLE EFFECTIVENESS OF MATHEMATICS), we had shown that the usually accepted views of Wigner and Gödel are questionable. The success of mathematics can only be attributed to "using strictly logical language of mathematical relations, set as cause-effect relating equations", as you put it. For this reason, we have pleaded for Physical Mathematics instead of Mathematical Physics in our essay this time. You also appear to agree when you say: "The limits in our discovering the ontological rules behind the biospheric and cosmo-spheric evolutions are not due to the equations alone; but from what input and output physical meaning we assign to the starting mathematical symbols and the connecting operators".
You are right that "the Cosmological Redshift is definitely not a Doppler Effect". But concluding that it indicates expanding universe may not be correct because of several reasons: 1) our observation in cosmic scales are insignificant, 2) blue-shift and galactic mergers have been observed, and 3) expansion is seen only in larger scales of galactic clusters and no less. If we look at everything from atoms to stars and galaxies, the universe may replicate the solar system with galactic clusters as planets around the Sun. This will imply a closed universe, but some cosmological models propose this also.
When you talk about "the '+' operator now implies real interaction between the particles followed by real energy exchange, followed by physical transformations (changes in excited states)", these do "give rise to measurable data if it happens inside a human constructed apparatus". However, we think there are some missing parameters we are not considering sufficiently. These include the "nature and source of the operator" and "what is an electron", which points you have also raised subsequently in the essay.
Regarding biological evolution, "the perpetual evolutions towards higher and higher forms of biological species" is a debatable proposition. What is meant by higher and higher? Evolution of intelligence within a species has not been proven, though there is an hierarchy with humans at the top. In fact, we are becoming more informative and less intelligent. Since "viruses and the bacteria just started evolving out of the inanimate atoms and molecules to the living species", they have not changed and are the same they used to be before 3.5 million years ego. There is plenty of literature, which discuss Desire, Belief, Faith, and Hope in depth. There is also much literature about mind and its functions, which are mechanical in nature and about which we have replied extensively to Dr. R. K. Singh's post in our thread.
Regarding Dark Energy and Dark Matter, you must be aware of the mismatch between theory and observation, which differ by a factor of 10^120. This is called the biggest mismatch in history. Though it has been narrowed down to 10^55, it is still too big to make a claim for a "theory". You have clearly demonstrated the deficiencies of the modern approach. Your modified approach and conclusion: "to incorporate the Interaction Process Mapping Epistemology (IPM-E) in physics" is significant and needs follow up research. We thoroughly enjoyed your essay.
Regards,
basudeba