A logical train of thought cannot exist in a vacuum. Without some premise, some basic assumption, logic has no ground from which to push off. If you make some statement about the world, or about life, and someone asks you to give your reasons, and then to give reasons for those reasons, and so on (as children at a certain age enjoy doing), you find that eventually you land on a simple assumption you have made about life, with no reasons to back it up. You might not even be aware that you had this assumption; it just exists implicitly in your mind.
The fundamental assumption about existence is critical. Something must be assumed to be eternal because if at any point there existed absolutely nothing, it is inconceivable that anything could ever exist after that point. Ex nihilo nihil fit. There is Something that must be taken as a base assumption always to have existed, with no reason behind it for existing.
For a theist, this Something is God, the divine Creator of matter, who transcends time and space, existing eternally. For an atheist, this Something is Matter. The physical universe, or its physical predecessor, simply always was. This should be absolutely clear: a theist cannot explain why God exists, and an atheist cannot explain why Matter exists. These are assumptions at the very core, from which all other reasons are derived. Many atheists are mistaken in thinking this to be a religious problem, but it is in fact an inherent limitation.
Isaac Newton in the 17th century arguably accomplished more to advance scientific knowledge than any single person in history. While Newton gave us the laws of motion, unveiled the mystery of gravitation, solidified the heliocentric model, exposed the nature of light and color, and invented the calculus, he argued against the view that the universe is reducible to Matter. “Gravity explains the motions of the planets,” he said, “but it cannot explain who set the planets in motion. God governs all things and knows all that is or can be done.”
In the modern era, however, the scientific view has slowly shifted into a Matter-oriented philosophy. Perhaps the transition is marked by Albert Einstein, the other arguably most accomplished scientist in history, who introduced general relativity in 1915 and developed the quantization of light into photons. Although agnostic about the origin of order and complexity in the universe, Einstein rejected the idea of a personal God.
Is there any particular reason for taking Matter or God to be a more valid assumption than the other?
This subject was sharply debated throughout the early and mid-20th century because a new scientific theory was amassing evidence that contradicted a materialistic worldview. The scientific community (including Albert Einstein) almost uniformly believed in a Steady State theory of the universe, that it was basically static and had eternally existed as we now see it. This supports the atheistic assumption of Matter.
However, two discoveries sent the Steady State theory into obsolescence. The first was the galactic redshift (observed by Vesto Slipher in 1912), a kind of Doppler Effect with light indicating that the universe in all directions accelerates outward. The second was the predicted observation of cosmic microwave background radiation (measured by Arno Penzias and Robert Wilson in 1964), a residual effect of an ancient cosmic explosion. What became known as the Big Bang theory gained acceptance.
It should not be lost to history that both sides of this argument acknowledged that the Big Bang was forcing theological questions into physics. Many scientists fought against the new theory for precisely this reason: they were fighting for their worldview, for their basic assumption about reality. Nevertheless, the Big Bang implies a beginning; it begs the question of what ethereal hand could have entered nothing to imbue it with the gift of everything.
A beginning implies a story. The reverberating evidence that supports this implication is man, a being who arose from within the story, readily able to appreciate the story. If Something deliberately authored our universe, our existence, then it stands to reason that there would be conscious readers like us who can grasp the plot and study its drama, its artistry, and its grandeur.
In the beginning, a point of infinite density and temperature exploded outward, giving birth to the universe, to matter and to time, to all the physical properties that enabled the elements, and stars, and galaxies, and the earth, and man; this explosion carries all the objects of the universe within its expansive force. Opponents of the Big Bang argued that it would bring religious implications into physics, and they were certainly correct. The most obvious conclusion is inescapable.
In the beginning God created the heavens and the earth.
In the beginning was the Word.