If there is a conflict between the Catholic understanding of how the world operates and that of some people in the scientific community, it is not a conflict over science per se but over the assumptions that people bring to scientific thought. A basic element of the scientific method is parsimony. This means that one always looks for the simplest understanding that adequately explains a phenomenon. The simplest explanation is usually the best one to make use of at a practical level. This says nothing about the actual nature of the phenomenon but is simply a methodological rule that scientists have found useful.
A philosophical position that has become popular since the Enlightenment is materialism. This is the position that science should only address that which deals with the material universe and that all phenomena in the material universe can be understood by resort to a more detailed understanding of matter. Materialism can be a useful methodological constraint on science, defining the limits of its competence to explore and explain. Some people however, treat materialism as a description of the nature of the universe, arguing that the limit of reality is the material universe. The possibility of the spiritual or any non-material reality is rejected out of hand, as an essential presumption of the materialist. Such a presumption is an act of faith, as much as a presumption that non-material reality exists.
Obviously, the Catholic scientists accepts the possibility of the spiritual and that in some way the spiritual has an impact on the material. For example, Pierre Teilhard de Chardin argues that evolution works through the biological processes of natural selection, adaptation to environmental niches and diversification. In this, he is taking the position of a respected, world class paleontologist. Yet, as a priest and theologian, he also argues that evolution moves in the direction of the Omega Point, which is the apex of biological development in which we are the image and likeness of God to the full extent of which biological life is capable. He sees a spiritual reality working through natural processes to draw life in the direction of its fulfillment. His position rejects nothing in science, while suggesting a purpose and direction to evolution. The absolute materialist would see nothing but the playing out of the laws of nature, which are inherent in the structure of the universe.
I have a great respect for science. I was trained in the scientific method as a young man and worked in the social sciences as a researcher for several decades. While not trained in the physical sciences I have read extensively and have an informed layman’s appreciation of those disciplines. I find great beauty and a powerful vision of the universe when considered from the scientific perspective. Scientific knowledge has transformed the world in which we live. In the past century scientific knowledge has grown to such an extent that our understanding of the universe has exploded. What was once attributed to spiritual influences can now we explained in material terms.
In a similar manner, what was once attributed to purely material reality is now understood as much more complex as once thought and may even overlap into areas that we can’t even begin to explain meaningfully. For example, quantum mechanics has taught us that consciousness plays a critical role in the material universe, yet what is consciousness and how can it influence the material universe? Over 90% of the known universe is comprised of “dark matter” and “dark energy”, yet we have no idea what “dark matter” or “dark energy” is. Perhaps, these are things that will eventually be explained purely by material phenomena but perhaps they are pointing to a reality that is beyond the limits of the material universe, which we do not understand but which we refer to nowadays as a spiritual or “supernatural” reality.
In any case, I find that being open to the full range of possibilities and examining all of them through the lens of the scientific method, realizing that this is a method for finding the most reasonable answers to our questions about the nature of the universe, is the most appealing way to try and understand the universe in which we find ourselves.