"Dear Rabbi, Scientific paradoxes are rooted in empirical data. And they may be eventually resolved with more data and improved scientific theories. Theological paradoxes are not rooted in empirical data, not rooted in scientific theory, but instead are rooted in religious dogma and the speculations of ancient superstitious peoples."
Rather than just respond directly I thought it might be instructive to offer a bit of a fuller treatment.
Scientists are biased too
It's obvious to this reader that science is superior to religion. Science, as he says, is rooted in empirical data. That, of course, is true, but not necessarily relevant. As I've written before in many places like here, here and here, scientific "facts" oftentimes have a shelf life and that what is accepted as indisputable fact today becomes tomorrow's phrenology.
Scientists are both significantly more biased than most people think and are getting caught more and more in fraudulent research due, in part, to that fact that they must publish in respected scientific journals to receive grant money, etc. Very little research outside of the currently established norms makes it to print so that the scientists are essentially coerced into printing what the establishment wants - and not what the empirical evidence suggests. Have a look at http://retractionwatch.com/ for a few good examples of that.
We could also do a little thought experiment. What if there was scientific evidence that supported basic theological claims about Creation, God or any other "dogma." Do you suppose that these scientifically-minded individuals would start keeping kosher or going to mass, etc? Or is it more presumable that they would ridicule the findings and quickly "debunk" them - no matter thoroughly and professionally the research was conducted? There is real research, for instance, that supports "Intelligent Design," Near Death Experiences (NDE's) and Bible Codes. These may or may not be true ideas, but naturally, they are summarily dismissed by the scientific majority as rank quackery while research on topics like fracking, climate change and GMO's are accepted as proven beyond all doubt despite a large body of conflicting evidence. See http://www.climatedepot.com/ for instance.
Science is only a methodology
The Scientific Method is a great tool (when untainted by bias) for improving our understanding of the natural world. It provides raw information. However, what that information means and how it may apply to our lives is the realm of philosophy - of which theology is one type. A scientist's skill in gathering information on a particular topic in no way gives him or her the ability to extrapolate or draw particular conclusions about that information. As such, both the scientist and the philosopher are making critical contributions towards humanity's general understanding of the nature of reality.
Theology has no Scientific Method in that it deals with ideas of transcendence that are the realm of metaphysics (ie: beyond physics). This is not to suggest that there is no rigor to it or that it can't contribute to our understanding of the physical (or non-physical) world. Theology helps us to understand that logical inferences can be drawn from our physical world that teach us about the nature of the non-physical - which is by definition non-empirical. So the suggestion that theology is somehow deficient since it doesn't (and can't possibly) function in the way that science does it simply false - like comparing apples to oranges. On the contrary, theology is essential for making any sense of what science discovers.
Just Some Speculations?
One might be tempted to ask if there is any empirical evidence to support our reader's supposition that the ancient and the superstitious were merely speculating. Is that a scientific fact or just an emotional position? There is an unfortunate phenomenon by which many people hubristically suppose that people who lived long ago were basically stupid. I wonder, when contemplating the distant future, of these same people pre-regard themselves as uninformed, backwards and ignorant as compared to our future progeny. I doubt it, but if they do I would think that it would give them some pause. Judaism tends to take the position that those who lived before us were mentally and spiritually superior - very much unlike most of our contemporaries. In any event, there was no shortage of geniuses who lived long ago. True, they did not create the Keurig Machine, but they may have had a pretty firm grasp of various aspects of the nature of reality - perhaps better than we do.
More often than not, people who buy into something tend to regard it as fact, proven, self-evident, etc. Those that do not think the opposite and tend to be irritated that others can't appreciate the simple and obvious logic of their position. Aspersions can certainly be cast on either group and as such it seems to me a better starting position would be one of mutual respect and understanding. Has religion truly contributed nothing to the world? Just some random speculations? Fortunately, there are many who can, and do, acknowledge the folly of those sentiments. Here's my favorite:
“Certainly, the world without the Jews would have been a radically different place. Humanity might have eventually stumbled upon all the Jewish insights. But we cannot be sure. All the great conceptual discoveries of the human intellect seem obvious and inescapable once they had been revealed, but it requires a special genius to formulate them for the first time. The Jews had this gift. To them we owe the idea of equality before the law, both divine and human; of the sanctity of life and the dignity of human person; of the individual conscience and so a personal redemption; of collective conscience and so of social responsibility; of peace as an abstract ideal and love as the foundation of justice, and many other items which constitute the basic moral furniture of the human mind. Without Jews it might have been a much emptier place.”
Thank God for all that ancient, superstitious speculation.