I have spent several weeks dialoguing with an atheist. There’s perhaps no better exercise to build one’s faith. The reason being is that irrationality is a sign itself of the supernatural, for confusion and spiritual blindness are hallmarks of the prince of darkness. There are some mysteries the atheist cannot solve, questions he cannot answer, and some aspects of human life and the origins of the universe that cannot be explained by science alone. But this he will deny by either ignoring the subject, minimizing the question at hand, or ignoring scientists who refute his position and only quoting those who do. He leaves many painful ironies in the wake of his “reasoning.”
THE SCIENTIFIC IRONY
Because the atheist refuses anything God, science in essence becomes his “religion.” That is, he has faith that the foundations of scientific inquiry or the “scientific method” developed by Sir Francis Bacon (1561-1627) is the process whereby all physical and supposed supernatural questions will eventually be resolved to be merely by-products of nature. The scientific method, you could say, is the atheist’s “ritual.” But the painful irony is that the founding fathers of modern science were nearly all theists, including Bacon:
It is true, that a little philosophy inclineth man’s mind to atheism, but depth in philosophy bringeth men’s minds about to religion; for while the mind of man looketh upon second causes scattered, it may sometimes rest in them, and go no further; but when it beholdeth the chain of them confederate, and linked together, it must needs fly to Providence and Deity. —Sir Francis Bacon, Of Atheism
I have yet to meet an atheist who can explain how men like Bacon or Johannes Kepler—who established the laws of planetary motion about the sun; or Robert Boyle—who established laws of gases; or Michael Faraday—whose work on electricity and magnetism revolutionized physics; or Gregor Mendel—who laid the mathematical foundations of genetics; or William Thomason Kelvin—who helped lay the foundation of modern physics; or Max Planck—known for quantum theory; or Albert Einstein—who revolutionized thinking in the relationship 
between time, gravity, and the conversion of matter to energy… how these brilliant men, all disposed to examining the world through a careful, strict, and objective lens could possibly still believe in the existence of God. How can we even take these men and their theories seriously if, on the one hand, they are supposedly brilliant, and on the other, completely and embarrassingly “stupid” by condescending to belief in a deity? Social conditioning? Brain washing? Clerical mind control? Surely these scientifically attuned minds could have sniffed a “lie” as big as theism? Perhaps Newton, whom Einstein described as a “brilliant genius, who determined the course of Western thought, research, and practice to an extent that nobody before since his time can touch” gives a bit of insight into what his and his colleague’s mindset was:
I do not know what I may appear to be to the world; but to myself I seem to have been only like a boy playing on the seashore, and diverting myself in now and then finding a smoother pebble or a prettier shell than ordinary, while the great ocean of truth lay all undiscovered before me... The true God is a living, intelligent, and powerful being. His duration reaches from eternity to eternity; His presence from infinity to infinity. He governs all things. —Memoirs of the Life, Writings, and Discoveries of Sir Isaac Newton (1855) by Sir David Brewster (Volume II. Ch. 27); Principia, Second Edition
Suddenly, it becomes clearer. What Newton and many earlier and later scientific minds had that many scientists lack today is humility. It was their humility, in fact, that enabled them to see with all clarity that faith and reason are not contradictory. The painful irony is that their scientific discoveries —which atheists hold in esteem today—were permeated with God. They had Him in mind when they broke open new dimensions of knowledge. It was humility that enabled them to “hear” what so many intellects today cannot.
When he listens to the message of creation and to the voice of conscience, man can arrive at certainty about the existence of God, the cause and the end of everything. —Catechism of the Catholic Church (CCC), n. 46
Einstein was listening:
I want to know how God created this world, I am not interested in this or that phenomenon, in the spectrum of this or that element. I want to know His thoughts, the rest are details. —Ronald W. Clark, The Life and Times of Einstein. New York: The World Publishing Company, 1971, p. 18-19
Perhaps it is no coincidence that as these men strove to honor God, God honored them by pulling the veil further back, granting them deeper understanding of the machinations of creation.
…there can never be any real discrepancy between faith and reason. Since the same God who reveals mysteries and infuses faith has bestowed the light of reason on the human mind, God cannot deny himself, nor can truth ever contradict truth… The humble and persevering investigator of the secrets of nature is being led, as it were, by the hand of God in spite of himself, for it is God, the conserver of all things, who made them what they are. —CCC, n. 159
LOOKING THE OTHER WAY
If you’ve ever dialogued with a militant atheist, you will soon discover that there is absolutely no evidence possible that will convince them of the existence of God, even though they say they are “open” to God proving Himself. Yet, what the Church calls “proofs”…
…the miracles of Christ and the saints, prophecies, the Church’s growth and holiness, and her fruitfulness and stability… —CCC, n. 156
…the atheist says are “pious frauds.” The miracles of Christ and the saints can all be naturally explained, they say. The modern miracles of tumors instantly disappearing, the deaf hearing, the blind seeing, and even the dead being raised? Nothing supernatural there. It doesn’t matter if the sun were to dance in the sky and change colors defying the laws of physics as happened at Fatima in front of some 80, 000 communists, skeptics, and the secular press… all explainable, says the atheist. That goes for Eucharistic miracles where the Host has actually turned to heart tissue or bled profusely. 
Miraculous? Just an anomaly. Ancient prophecies, such as the some four hundred or so that Christ fulfilled in His Passion, Death, and Resurrection? Manufactured. M odern prophecies of the Blessed Virgin that have come true, such as the detailed visions and predictions of slaughter given to the child seers of Kibeho before the Rwandan genocide? Coincidence. Incorruptible bodies that exude fragrance and fail to rot after centuries? A trick. The Church’s growth and holiness, which transformed Europe and other nations? Historical nonsense. Her stability throughout the centuries as promised by Christ in Matthew 16, even in the midst of pedophile scandals? Mere perspective. Experience, testimonies, and witnesses—even if they number in the millions? Hallucinations. Psychological projections. Self-deception.
To the atheist reality means nothing unless it has been probed and analyzed by man-made tools that a scientist has put faith in as being the definitive means of defining reality.
What is astounding, really, is that the atheist is able to overlook that many brilliant minds in the fields of science, education, and politics today not only believe in God, but many have converted to Christianity from atheism. There is a kind of intellectual arrogance at play where the atheist sees himself as “knowing” while all theists are essentially the intellectual equivalents of face-painted jungle tribesmen stuck in ancient mythologies. We believe simply because we cannot think.
It brings to mind the words of Jesus:
If they will not listen to Moses and the prophets, neither will they be persuaded if someone should rise from the dead. (Luke 16:31)
Is there another reason why atheists seem to look the other way in the face of overwhelming supernatural evidence? One could say we are talking about demonic strongholds. But not everything is demonic. Sometimes men, endowed with the gift of free will, are simply proud or stubborn. And sometimes, the existence of God is more an inconvenience than anything else. Grandson of Thomas Huxley, who was Charles Darwin’s colleague, said:
I suppose the reason we leaped at the origin of species was because the idea of God interfered with our sexual mores. —Whistleblower, February 2010, Volume 19, No. 2, p. 40.
Professor of philosophy at New York University, Thomas Nagel, echoes a sentiment common among those who hold unswervingly to evolution without God:
I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers. It isn’t just that I don’t believe in God and, naturally, hope that I”m right in my belief. It’s that I hope there is not God! I don’t want there to be a God; I don’t want the universe to be like that. —Ibid.
At last, some refreshing honesty.
REALITY DENIER
The former chair of evolution at the University of London wrote that evolution is accepted…
…Not because it can be proved logically coherent evidence to be true but because the only alternative, special creation, is clearly incredible. —D.M.S. Watson, Whistleblower, February 2010, Volume 19, No. 2, p. 40.
Still, despite the honest criticism by even evolution’s proponents, my atheist friend wrote:
To deny evolution is to be a history denier akin to those who deny the holocaust.
If science is the atheist’s “religion” so to speak, evolution is one of its gospels. But the painful irony is that many evolution scientists themselves admit there is no certainty as to how the the first living cell was created let alone the first inorganic building blocks, or even how the “Big Bang” was initiated.
The thermodynamic laws state that the sum total of matter and energy stays constant. It is impossible to create matter without expending energy or matter; it is similarly impossible to create energy without expending either matter or energy. The second law of thermodynamics states that total entropy is inevitably increasing; the universe must move from order toward disorder. These principles lead to the conclusion that some uncreated being, particle, entity, or force is responsible for creating all matter and energy and for giving an initial order to the universe. Whether this process occurred through the Big Bang or through a literalist’s interpretation of Genesis is irrelevant. What is crucial is that there must exist some uncreated being with the ability to create and give order. —Bobby Jindal, Atheism’s Gods, Catholic.com
And yet, some atheists insist that “to deny evolution is to be on par intellectually with a holocaust denier.” That is, they have put a radical faith in something they cannot prove. They trust absolutely in the power of science, like it were a religion, even when it is powerless to explain the inexplicable. And despite the overwhelming evidence of a Creator, they insist that the first cause of the universe just cannot be God, and in essence, abandon reason out of bias. The atheist, now, has become the very thing he despises in Christianity: a fundamentalist. Where one Christian may cling to a literal interpretation of creation in six days, a fundamentalist atheist clings to his belief in evolution without concrete scientific evidence… or in the face of the miraculous, cleaves to speculative theories while discarding the plain evidence. The line dividing the two fundamentalists is thin indeed. The atheist has become a reality denier.
In a potent description of the irrational “fear of faith” present in this kind of thinking, world-renowned astrophysicist Robert Jastrow describes the common modern scientific mind:
I think part of the answer is that scientists cannot bear the thought of a natural phenomenon which cannot be explained, even with unlimited time and money. There is a kind of religion in science, it is the religion of a person who believes there is an order and harmony in the universe, and every effect must have its cause; there is no First Cause… This religious faith of the scientist is violated by the discovery that the world had a beginning under conditions in which the known laws of physics are not valid, and as a product of forces or circumstances we cannot discover. When that happens, the scientist has lost control. If he really examined the implications, he would be traumatized. As usual when faced with trauma, the mind reacts by ignoring the implications—in science this is known as “refusing to speculate” —or trivializing the origin of the world by calling it the Big Bang, as if the Universe were a firecracker… For the scientist who has lived by faith in the power of reason, the story ends like a bad dream. He has scaled the mountain of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries. —Robert Jastrow, founding director of NASA Goddard Institute for Space Studies, God and Astronomers, Readers Library Inc., 1992
A painful irony, indeed.
