I think that if there is one truth that people need to learn, in the world, especially today, it is this: that the intellect is only theoretically independent of desire and appetite in ordinary, actual practice. It is constantly being blinded and perverted by the ends and aims of passion, and the evidence it presents to us with such a show of impartiality and objectivity is fraught with interest and propaganda. We have become marvelous at self-delusion; all the more so, because we have gone to such trouble to convince ourselves of our own absolute infallibility. The desires of the flesh–and by that I mean not only sinful desires, but even the ordinary, normal appetites for comfort and ease and human respect, are fruitful sources of every kind of error and misjudgement, and because we have these yearnings in us, our intellects (which, if they operated all alone in a vacuum, would indeed, register with pure impartiality what they saw) present to us everything distorted and accommodated to the norms of our desire.If we get our minds around what Merton is saying here it will rock our world. We can't trust our own thinking. We need our reason to be checked against something. Pure science gives us that. Ideas are tested by experiments. Even conclusions we are very certain of need to be discarded if they don't fit the data. We need that. Before we developed the scientific method the knowledge of the natural world grew very slowly. Reason alone just takes too many wrong turns.
When we get away from pure science into social science, morality, philosophy or even theology then our reasoning gets progressively less testable. The experiments are not precise and we get into endless discussions about methodology. As we get further and further into the realm of human choices and what they mean we lose the science. We are back down to pure reason and we don't do well. We still have great confidence in our logic. We are just wrong a lot.
Some say that it is only a matter of time before science becomes able to test our reason in all areas. That will only be true if humans are not actually capable of making choices. If every human thought and every human decision can be predicted 100% by analyzing the physical inputs then science at least has a chance of analyzing it all. But what if that is not true? What if people really do make free choices? That is a human person is more than their body chemistry, their brain processes, the sum of their inputs? What if we are not at the mercy of the physical world but actually have some power to act on it?
Then science would have a barrier. It would not just be a barrier of complexity but a more principled barrier. That human behavior simply could not be fully described by science because humans make real choices. They are capable of doing good and capable of doing evil. Then science will never be able to describe your marriage like it can describe photosynthesis.
In approaching this question logically we are firmly in one of those areas that Merton says is "fraught with interest and propaganda." Where our reason tends to be distorted. What is up for debate is the very essence of who we are. How can we not be biased? Biases can run both ways.
Merton found an answer in Jesus Christ and in the Catholic church. That is why he became a monk. Not to stop reasoning but to have something to check his reason against. More than that, he wanted to control those appetites that infected his reason. Through a sacramental, prayerful, and holy life he could keep the "desires of the flesh" under control and be truly rational.