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Stating that man reasons and is farther developed than other animals requires the affirmation of "non-physical" 'evolution' (if you will), yet the materialist, physicalist denies there is anything other than the physical. Thus they must deny reason, rational thought, and logic to be consistent with their Weltanschauung.

And yet we know they do not deny reason, rational thought, or logic. (If they did, they'd be out of a job.) They just refuse to acknowledge the fundamental authority, the basis for the legitimacy of reason, rational thought, and logic. This basis cannot be observed in the phenomenal world for the simple reason that it transcends the phenomenal world. Which sort of thing the physicalist/materialist rejects out of hand: NOTHING transcends the physical world, the world of direct observables. Thus he's in a deep pickle without even being aware of it — for he delegitimates the very foundations of his own thinking.

In an earlier post on another thread, Texas Songwriter, you wrote, "science and philosophy are inextricably linked. In fact it is impossible to 'do science' apart from philosophy, because no one, especially science, approaches a scientific problem apart from their worldview. That is why fidelity to truth is so important. If one's faithfulness is to one's worldview, irrespective of truth, progress is impossible."

I so agree!

And yet science and philosophy have been relentlessly delinked in recent times. Science thinks it can work without philosophy even though its initial premises and its methods depend on it. Yet by excluding the sector of reality that philosophy addresses — universals, non-corporeals (like logic, reason, natural laws), etc. — science both limits itself to a partial and incomplete view of the Whole which we call the universe, and puts itself into a position whereby it cannot even explain its own modus operandi.

I try to work within a "whole systems" approach to Nature, which is a legacy to me from Pythagoras (~600 B.C.), the father of whole systems theory. The Pythagorean approach integrates mathematics, psychology, ethics, and political philosophy into one integrated whole.

...[T] central focus of Pythagorean thought is in many respects placed on the principle of harmonia. The Universe is One, but the phenomenal realm is a differentiated image of this unity — the world is unity in multiplicity. What maintains the unity of the whole, even though it consists of many parts, is the hierarchical principle of harmony, the logos of relation, which enables every part to have its place in the fabric of the all....
Pythagoras, no doubt, would have disapproved of the radical split which occurred between the sciences and philosophy during the 17th century "enlightenment" and which haunts the intellectual and social fabric of Western civilization to this day. In retrospect perhaps we can see that man is most happily at home in the universe as long as he can relate his experiences to both the universal and the particular, the eternal and the temporal levels of being.
Natural science takes an Aristotelian approach to the universe, delighting in the multiplicity of the phenomenal web. It is concerned with the individual parts as opposed to the whole, and its method is one of particularizing the universal. Natural science attempts to quantify the universal, through the reduction of living form and qualitative relations to mathematical and statistical formulations based on the classification of material artifacts.
By contrast, natural philosophy is primarily Platonic in that it is concerned with the whole as opposed to the part. Realizing that all things are essentially related to certain eternal forms and principles, the approach of the natural philosopher strives to understand the relation that the particular has with the universal. Through the language of natural philosophy, and through the Pythagorean approach to whole systems, it is possible to relate the temporal with the eternal and to know the organic relations between multiplicity and unity.
If the scientific spirit is seen as a desire to study the universe in its totality, it will be seen that both approaches are complementary and necessary in scientific inquiry, for an inclusive cosmology must be equally at home in dealing with the part or the whole. The great scientists of Western civilization — Kepler, Copernicus, Newton, Einstein, and those before and after — were able to combine both approaches in a valuable and fruitful way....
Today, in many circles, to a large part fueled by the desire for economic reward, science has nearly become confused with and subservient to technology, and from this perspective it might be said that the ideal of a universal or inclusive science has been lost. This is because the ideal scientist is also a natural philosopher who is interested in relating his discoveries to a larger universal framework, whereas the dull-minded technologist, if he has any interest in universal principles at all, limits that interest to their specific mechanistic applications rather than their intrinsic worth of study. Yet, those who study universal principles as principles-in-themselves, often find that these principles have many applications in a wide variety of fields.
While Pythagoras would have taken a dim view of this artificial and dangerous split between science and philosophy, the negative consequences of this rupture have not gone unnoticed. Yet with his emphasis on the unity of all life, Pythagoras would have been in an excellent position to foresee the negative consequences: ecological imbalance, materialism, the varied effects of personal greed, the disintegration of human values, the decline of the arts, a lack of interest in personal excellence and achievement. In a sense these problems, not necessarily unique to this age, result from a lack of balance and an ability to see the parts in relation to the whole. [from The Pythagoran Sourcebook and Library (1987), David Fideler, ed., "Introduction," p. 43f]

I very much admire C.S. Lewis' (truthful!) answer to the question of whether he had a soul: He said "I am a soul."

Indeed, the soul — as "the form of the body" — takes precedence over the body. But science nowadays only studies "bodies."

Texas Songwriter, thank you so very much for your outstanding essay/post!