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Nevertheless, the central issue that the current paradigm is inadequate to investigate living systems can be seen from any of these perspectives.... Only one with fingers in his ears, humming, stomping, gritting his teeth and thus refusing all insights could possibly miss it.

Oh so true, dearest sister in Christ!

Perhaps part of the problem is the increasing specialization of science nowadays. Even the specialties have sub-specialties — all premised on the Newtonian Paradigm (because that's supposedly what science "is"). Everyone is trying to see through the peephole of his own specialization, and increasingly the big picture is lost from view. Because of the loss of the big-picture view, people do not see that contradictory to its claim, the Newtonian formalism is not the "largest model" of the universe, wherein physics is basic, and biology a "special case" of physics.

To turn that around, it seems to me that the "largest model" would not treat biology as a "special case." As relatively rare as biological organisms apparently are in the universe, they display unique behaviors — i.e., behaviors not found in the inorganic world — that any "largest model" would have to be able to "map to" Reality in order to be the "largest" model. Contemporary science hits the wall precisely here: The Newtonian formalism is no help in accounting for or explaining the organizational and functional behavior of living systems. That behavior does not reduce to particle motions alone. What is important is the relations obtaining between particles and with the systems they constitute. We are speaking of the intangible organizational principles (i.e., systems of causal entailment) at work in living systems. Newtonian science has no method for getting at this problem.... E.g., since the entire idea of final cause has been banished from "respectable" science, there is no logical way to explain what we even mean by "function." And that's just one problem with the status-quo thinking....

But since the 1930s, some really first-rate mathematicians cum physicists cum theoretical biologists (notice the multidisciplinary approach) have been working on it; e.g., Ervin Bauer, Nicolas Rashevsky, and most recently Robert Rosen. Mainly their work has not been much acknowledged, let alone appreciated, by most of their eminent contemporaries....

But that may be about to change. I notice that some theoretical biologists are beginning to "play with" some of Robert Rosen's ideas; e.g., the Kinemans.

Thank you so very much for your excellent essay/post, dearest sister in Christ!