Dear Ilgaitis.
Thank you very much for your detailed, deep answer, reading my essay and questions.
1. About the "Logos" and "spirit." You noticed that I took only the first part of the line from Evagelia from Ionne in Greek: "In the Beginning was the Logos ...". From the dictionary of the ancient Greek language I. Dvoretsky, the concept of "logos" has 34 clusters of meanings and each bush of meanings has three more meanings. Since I consider only Nature (Creation), I took the extremely general meaning of the concept of "logos" for Nature and Society - the "Law", that is, the extremely general Law of Nature (First Law, "Law of laws"). "LOGOS" is the law of the whole primordial being, the primordial law of the Universe as a process of generation of meanings and structures. Notice that I put "meaning/sense" in the first place, and only then "structure". Sense is a way of existence of content, the foundation of being (Hegel). Now, in order to overcome the crisis of understanding, the task is "grasp" the essential (ontic) structure of the "LOGOS» (First Law) as an ontological "framework", ontological "carcass" and ontological "foundations" of Nature's being as an holistic process of generation of meanings and structures. What is needed here is a new extremely general understanding of "matter" in the spirit of Plato, its unification across all levels of the Universum as an holistic process: matter is that from which all FORMS are born. Form is the first entity (Aristotle). What holds the Primary structure (primordial generating structure)? Here I introduce a super concept: ONTOLOGICAL (COSMIC, STRUCTURAL) MEMORY as the "soul" of matter. The information revolution pushes physics to introduce the concept of "ONTOLOGICAL MEMORY" into the conceptual core of the Universum. Conceptual- paradigmatic problems of modern physics, uncertainty in philosophical (ontological) require the introduction of this super-noumenon, which clarifies the primordial structure of the Universum, clarifies the nature of the phenomenon of "information" and its place in the scientific picture of the world.
The principle of "triunity" as an ontological "Principle of principles", the generating principle, I consider only in relation to Nature (Creation). I only observe Nature, its "generating structure". The Russian language and the concept of "structure / строение" push towards the logic of triunity. And of course, the whole history of dialectical thinking. The ontological (ultimate) triunity in Nature is the triunity of the absolute (unconditional) forms of the existence of matter (absolute states): absolute rest (linear state) + absolute motion (movement in a "circle", vortex) + absolute becoming (wave state ). The absolute rest of matter was ejected, as I noted, from the scientific picture of the world. Therefore, problems arose with understanding of Nature, the problems of "grasping" its primordial structure. The paradigm of the world (Universum) as a whole should be included here. "Equations" is always a "clipping" from the being of the Universum as a whole.
2. I will try to answer your questions:
The first question. The task of Science is to explore Creation (Nature). But Man, on the basis of free will given to him by the Creator, has the right to guess the Creator's thought before the Act of Creation.. Different eras and cultures represent the Creator in different ways. It is also free will.
The second question. "LOGOS" sets the basis for knowledge only (framework, carcass, foundation), shows only ontical limits for thinking. The task of thinking is to look for ways to create new meanings and structures (material-ideal). The primordial generative structure expands the "framework" of modern, primarily linear thinking, introduces a new heuristic into the philosophical basis of fundamental science.
You gave good examples from the history of the development of technology. As an engineer who is interested in the philosophical foundations of fundamental science, the history of its formation, I can only say that if two scientific programs - Descartes and Newton - developed in parallel and had financial and intellectual support from the side of power structures, then the television could have appeared in 19 -th century ... In science, competition of trends and ideas should be maintained. The intellectual mainstream is dangerous for science and creativity, it leads to stagnation in scientific research.
You recalled Newton and Einstein. I agree with that. But Newton's metaphysics also requires a critical review (space and time). At the same time, it is good to recall Newton's religious views. The author of a biography published in 1924, L.T. Moore, attributed Newton's views to the radical form of anti-Trinitarianism -- Unitarianism. (Wikipedia) ... I think the thought of the Creator always helps the researcher of Nature (Creation). And here a good helper in the knowledge of Creation and the Creator is "the mother of all sciences" - Philosophy.
The holistic paradigm requires the unity of knowledge and faith. I believe that only the "Logos" understood as the "First Law" ("Law of laws") makes it possible to achieve such unity and the construction of the primordial (ontological) structure of the Universe as an eternal process of generating ever new meanings and structures.
Kind Regards,
Vladimir