Is scientific thought truncated?

From Chapter 6, Answers to Misgivings, in C. S. Lewis's Miracles: A Preliminary Study, pp. 41-42.

C. S. Lewis: All these instances show that the fact which is in one respect the most obvious and primary fact, and through which alone you have access to all the other facts, maybe precisely the one that is most easily forgotten—forgotten not because it is some remote or abstruse but because it is so near and so obvious. And that is exactly how the Supernatural has been forgotten. The Naturalists have been engaged in thinking about Nature. They have not attended to the fact that they were thinking. The moment one attends to this it is obvious that one’s thinking cannot be a merely natural event, and that therefore something other than nature exists. The Supernatural is not remote and abstruse: it is a matter of daily and hourly experience, as intimate as breathing. Denial of it depends on a certain absent-mindedness. But this absent-mindedness is in no way surprising. You do not need—indeed you do not wish—to be always thinking about windows when you are looking at gardens or always thinking about eyes when you are reading. In the same way the proper procedure for all limited and particular inquiries is to ignore the fact of your own thinking, and concentrate on the object. It is only when you stand back from particular inquiries and try to form a complete philosophy that you must take it into account. For a complete philosophy must get in all the facts. In it you turn away from specialised or truncated thought to total thought: and one of the fact total thought must think about is Thinking itself. There is a tendency in the study of Nature to make us forget the most obvious fact of all. And since the Sixteenth Century, when Science was born, the minds of men have been increasingly turned outward to know Nature and to master her. They have been increasingly engaged on those specialized inquiries in which truncated thought is the correct method. It is therefore not in the least astonishing that they should have forgotten the evidence for the Supernatural. The deeply ingrained habit of truncated thought—what we call the “scientific” habit of mind—was indeed certain to lead to Naturalism, unless this tendency were continually corrected from some other source. But no other source was at hand, for during the same period men of science were becoming metaphysically and theologically uneducated.

VR: This is an old post on the claim that scientific thought is truncated. I want to focus on that claim, rather than on the claim that if we think about our thinking, it is obvious that the AFR is correct. I am linking back to the original DI discussion.