For example, the universe should not manifest itself as a mathematically structured entity and it would not contain any conscious being; since I am a physicist, let me try to explain these points from a scientific point of view.
The existence and the goodness of God is the most fundamental truth and I do not think we can deduce such truth from some other truth, because this would mean that we believe more in the other truth than in God. I believe in God because the certainty of His existence is in me and I feel His Presence, expecially during prayer. Nevertheless, I think there are solid rational arguments which confirms my beliefs.
All what science shows about the physical reality is that it manifests itself as a realization of some specific abstract mathematical models (what we call “the laws of physics”); in fact, the subatomic components of matters (quantum particles and fields) are actually only abtract mathematical concepts. On the other hand, mathematical models are only constructions of the rational thought and a mathematical model can exist only as a thought in a thinking mind conceiving it; this implies that matter (and the physical reality) is not the foundation of reality, but its existence depends on a more fundamental reality i.e. consciousness: contrary to the basic hypothesis of materialism, consciousness is a more fundamental reality than matter.
Therefore the existence of this mathematically structured universe implies the existence of a conscious and intelligent God, conceiving it as a mathematical model. In other words, the universe can be only the manifestation of a mathematical theory existing in the mind of a personal God.
I think that atheism does not account for such fundamental scientific information about the physical reality and denies, without any rational arguments, the only rational explanation.
There is another argument from physics that I find strongly convincing; according to our scientific knowledges, all chemical and biological processes (including cerebral processes) are caused by the electromagnetic interaction between subatomic particles such as electrons and protons. Quantum mechanics accounts for such interactions, as well as for the properties of subatomic particles. The point is that there is no trace of consciousness, sensations, emotions, etc. in the laws of quantum mechanics (as well as in all the laws of physcis). Consciousness is irriducible to the laws of physics, while all cerebral processes are. This is for me the most convincing scientific argument against materialism (which identifies cerebral processes as the origin of consciousness) and in favour of the existence of the soul, as the unphysical and trascendent principle necessary for the existence of our consciousness. Since our soul cannot have a physical origin, it can only be created directly by God. The existence of God is a necessary condition for the existence of our soul, as well as for the existence of us as conscious beings.