To think is to heed the essential. In such heedfulness essential knowing resides. What we usually call knowing is being acquainted with something and its qualities. In virtue of these cognitions we master things. This mastering knowledge is given over to a being at hand, to its structure and its usefulness. Such knowledge seizes the being, dominates it, and thereby goes beyond it and constantly surpasses it. The character of essential knowing is entirely different. It concerns the being in its groundit intends Being. Essential knowing does not lord it over what it knows but is solicitous toward it. For instance, to take just one example, every science is a cognitive mastering and outdoing and a surpassing, if indeed not a complete bypassing, of a being. All of which occurs in the manner of objectivization. Versus this, essential knowing, heedfulness, is a retreat in the face of Being. In such retreating we see and we perceive essentially more, namely something quite different from the remarkable procedure of modern science.
Heidegger, Martin Parmenides [Indiana,1992, Schuwer & Rojcewicz trans. p.3-4]
All great philosophers have wished to elevate philosophy to the rank of a science, which implies an admission in the deficiency of the respective philosophynamely, that it is not yet a science. One therefore orients oneself toward a rigorous scientific philosophy. Is rigor a super-scientific concept? Originally, the concept and sense of rigor is philosophical and not scientific; originally, only philosophy is rigorous; it possesses a rigor in the face of which the rigor of science is merely derivative.
Heidegger, Martin The Phenomenology of Religious Life [Indiana, 1995, 2004; Fritsch, Matthias & Gosetti-Ferencei, Jenifer Anna trans. p. 7]
Taking scientific method applying it to epistemology, ontology, aesthetics, metaphysics, ethics, theology and other non-scientific philosophical disciplines is dubious at best: its only justification would be if it worked. One problem is that not only science was applied: Humanism and Atheism tagged along for the ride, or were primary in the thought of the philosophers who were using science to justify their ideology, and now we think of Science as Humanism and Atheism in practice, or derivative of them.
Making Science, or Man or Irreligion or the State instead of infinite divine mystery the ultimate Truth around which all else must orbit really does discombobulate Western thinking and Western civilization - including science.
No atheistic or humanistic metaphysics has ever been successful logically. All end up opposing science (see Higher Superstition: The Academic Left and its Quarrels with Science by Levitt and Gross re the assault upon science and logic academically). Just look at Relativism and Post-Modernism etc today: all oppose Logic due to the inevitable conclusion it must reach concerning divine mystery.
We have adopted the old Sophist line of "Man is the measure of all things" then wonder why our logic doesn't apply to the real world beyond us anymore, and the science that grew from opposing such Sophistry.
Science itself is not to blame: the underlying assumptions of atheism and humanism are not so blameless. That we assume science must be atheistic or humanistic is the falsehood that needs to be corrected.
Why do scientists need to assume the non-existence of God? Why not just perform scientific inquiry and experimentation with minds open to all explanatory possibilities, with no thought to prove or disprove theological (and therefore non-scientific) issues?
