I had been listening to a friend who is Baptist having an argument with an atheist. It was hard, but I was staying silent through the entire thing. What was annoying to me was that I disagreed with both of them at various points. Sometimes, my friend would make a good point about God as Creator, and sometimes the atheist would make a good point about scientific discovery. Yet, neither of them was exactly correct in their position. My friend knew I am not Baptist so he was not sure I was on his side, and the other gentleman knew I was not an atheist so he was sure I was not on his side.
Essentially, they were both coming at the subject from their own personal presuppositions, assuming that they had all the knowledge that was necessary to determine certain subjects. The Baptist was saying "nothing but the Bible" and the atheist was saying "nothing but science". This is where they were both wrong. Aside from the disagreements between the baptist view of theology and the Catholic view, there are a number of problems with the idea of "only the Bible". When the atheist knows those problems, he is not going to accept what the baptist says. There are also a number of problems with the idea of "only science", and when someone knows those problems, he will not accept the atheist position.
It is common for many Catholics to respond to this entire issue with the perspective of "why not both?" There is some merit to this idea, after all, both the Bible and science come from God. On the surface, this sounds like a proper way of dealing with the situation (at least for those of us who accept the divine origin of the Catholic Church). Yet, there are some significant problems with this idea, and there are few today who recognize what they are.
Let us take first the circumstances with the idea "just the Bible". Most of my readers will likely agree with the Catholic criticism that there must always be some form of interpretation, and that we can never truly ever have "just the Bible". Since someone has to interpret what is read there is always an opinion of the words of the Scriptures, and never a raw, uninterpreted, truth. If a Baptist reads the Bible he will interpret it in accord with his baptistic principles that he believes. If an atheist reads the Bible he will interpret it in accord with what he believes.
Most Catholics know well that the only way that God has given us a perfect interpreter of holy writ is in the unbroken Tradition that has been handed down for 2000 years. Just because someone says "the Bible says..." does not mean that they have interpreted it correctly. They may say "the Bible says that Jesus is just a good person, but not divine"; that does not make it true. To imagine that every time anyone says "the Bible says" that he is speaking infallibly is absolute chaos, for there are millions of interpretations that contradict each other about what "the Bible says" in the world today. I think this point is fairly easy to grasp (even if one disagrees with it).
We have to be fair, however, and apply the same principle appropriately. Just as we know that not all interpretations of the Bible are necessarily accurate, so also we need to acknowledge that not all interpretations of science are perfectly accurate (this is why something is supposed to remain a "theory" until it has been proven). How many times has a scientist said "science has proven..." only to have the theory changed just a few years later? Therefore, whenever someone says "science says", we have to realize that he is giving an interpretation of what he sees in science, and not the perfect revelation of eternal truth. In principle, the study of science refers to that proper observation of the created world (and never the perfect interpretation of it).
There is nothing about the study of science that makes the scientist a perfectly neutral observer (though they really try to convince us that they are!). The scientist brings his presuppositions with him to scientific examination just as much as the theologian brings his. An honest scientist will admit that there is no such thing as a "bare fact". How many times have we heard those arguing for the "scientific" position that "science says, such and such" with the foolish idea that science is perfectly neutral and never subject to personal interpretation (the arrogance is staggering when you think about it). An atheist will interpret scientific observations according to an atheist view of the world; should we expect him to interpret science in accord with Catholic dogma? Of course not. We should expect him to deny Catholic dogma to a certain degree.
If the atheist (and the pagan, the buddhist, the muslim, etc.) are giving us their interpretation of science, then why do we trust them to tell us what is right if we know that they deny some of the most fundamental principles of truth (as revealed by Christ through His Church)? In my experience, it seems that many Catholics will be critical of protestant interpretations of the Scriptures, but show no discernment about non-Catholic interpretations of science. That is quite a foolish choice when you realize that (though they do make bad interpretations) protestants are often much closer to the truth than are atheists and pagans! Remember the scientists people trust in so many areas are the same ones telling us that the unborn child is just "a blob of tissue" and that homosexual behavior is "personal choice".
In fact we must go one step further: science is always on shaky ground (since it can always be changed by a new discovery), but the Church's interpretation of the Scriptures are never shaky--they remain true forever. This should impact us greatly, and even cause us to change our perspective on a number of issues. To give "science" the upper-hand over the Church's declaration of truth (especially those declarations that have been around longer than modern scientific study) because it is supposed to be "neutral" (when it should be obvious that it never is) is to let go of the authority of the Church. That is something, as a Catholic, that I am not willing to do.
Is this the way that our Lord Jesus wants us to learn about God's world--through the interpretations of those who deny God exists? Can an atheist give us a proper interpretation of something in science? Yes, it is possible; I am not saying it is not. Yet, protestants can give proper interpretations of the Scriptures, but they are not (supposed to be) allowed to be teachers in the Church. How then should we learn science? Whether taught by a Catholic or atheist (or otherwise), let us be cautious and critique their opinions with that which we know the Church affirms as undeniable truth. We are always to see the world (especially in science) through the eyes of the Church, and always for the glory of God above all else.