So what once seemed common sense must now be justified against modern, skeptical ways of thinking. But the justification can be made and the absurdities are only apparent ones - The contradictions are only paradoxes. Unfortunately the only way I can think to explain the religious way of thinking is through quantum mechanics. Now quantum mechanics seems perfectly understandable to me since I have a degree in physics, but it is just a great mystery to the vast majority of people. As a result I will try to keep the quantum mechanics to the absolute minimum and no real understanding of it is needed to read this paper.
Now the mysteries of Christian faith that might seem strange do not need to be listed as length, the Trinity will suffice as an example of all the mysteries. This doctrine of the Trinity says that there is only one God, but that The Father, Jesus and the Holy Spirit are all God. They are not just three aspects of God, but three persons, so that Jesus can talk to the Father since the Father is a distinct person from the Son. But that does not mean that they are three separate Gods, instead they are three persons of the one Godhead. So there is only one God but in three persons.
If your head swam a bit after reading that then you are not alone. Many parts of doctrine are of a similar nature and I've had many such experience when trying to absorb the mysteries of the faith. But, fortunately, the questions you are probably now asking have already been asked by some of the greatest minds to ever live. Not everyone blindly accepts what they are taught and the greatest theologians are precisely those who were troubled by the mysteries and had to examine them logically. The only real difference between our times and those of St. Augustine and St. Thomas Aquinas is that nowadays everyone questions the sort of ideas you find in Christianity.
But the Church is not alone in using the special type of reasoning that I will try to explain. Physicists also use this `Transcendent' reasoning when dealing with quantum mechanics. As an example, any physicist will confirm that an electron is both a particle and a wave. Now a wave is something that spreads out. When a wave passes through a breakwater it will bend around the breakwater and the previously straight wave will become rounded at its ends - The wave spreads out, that is what a wave is. But a particle does not spread out. If you shoot a cannonball through the gap in a a breakwater it will just keep on going in a straight line. The cannonball will not spread out like the wave since to be a particle is to not spread out. So this is what a physicist has to say about electrons: An electron is a wave, it is something that spreads out; but an electron is also a particle, it is something that does not spread out.
What was explained in the previous paragraph is quite plainly absurd. If an electron is a particle then that precludes it from being a wave and visa versa. Yet physicists assert that an electron is both a particle and a wave and they assert it for good reason - It is true. So how are we to explain this contradiction? The explanation is that physicists have been very sloppy in their way of speaking and should instead take a leaf out of the Church's book. The Church has much experience in this form of reasoning and to a theologian it should be clear what the answer is. Namely, an electron is neither a wave nor a particle. An electron is very much like a particle, but it is not a particle. An electron is very much like a wave, but it is not a wave.
To add to the confusion physicists will confirm that an electron takes every path to its destination and then, on having reached its destination, `chooses' a single path that it has taken to its destination. That is, it only takes a single path to its destination, but which path it has taken is not chosen until after it has already taken every path to its destination. This is an even more absurd explanation of an electron, but it can be explained as follows: An electron is very much like something that takes only one path to its destination, but it is not something that takes only one path to its destination; An electron is very much like something that takes every path to its destination, but it is not something that takes every path to its destination; And an electron is very much like something that decides what path to take after the journey is over, but it is not something that decides what path to take after the journey is over.
I doubt that really cleared things up for you much. But it does at least demonstrate that a certain type of skeptic is hypocritical. This particular type will blindly accept quantum mechanics, but then turn around and laugh at the faithful who use exactly the same form of reasoning.
The type of reasoning in question being that which makes use of analogies. That is, when a physicist talks of an electron being both a wave and a particle he should really say "An electron is analogous to a particle, but is not a particle. It is also analogous to a wave, but it is not a wave." The physicist is using analogies to describe something that he can't describe otherwise.
The reason the physicist has to talk like this is that we can only describe the world we see with our eyes and feel with our hands. But no-one has seen an individual electron, just a stream of them in a lightening bolt or spark. Now it would be nice if we could describe an electron precisely in terms of those things we see all around us, but there is no more reason why an electron should be just like a cannonball than there is that a cannonball should be just like a wave. And when physicists examined the quantum world they found that, to their confusion, it was completely unlike the world we see around us. But since we can only describes things in terms of what we can see and feel we have to describe an individual electron (Which no-one has seen or felt) in terms of what we can see and feel. That is, we have to use analogies that probably won't fit together properly and may seem contradictory. Hence we get the seemingly irrational description of an electron being both a wave and particle at the same time. Or worse, that an electron takes every path to its destination and then decides which single path it has taken.
Whenever we have to talk about something that you can't see or feel, we say that it transcends our experience. Quantum mechanics is partially transcendent, since it is still a part of this world and we can still examine it with our reason. But God is completely separate from His creation and therefore He is completely transcendent. Which is to say, He transcends not just our experience, but our reason as well. It is therefore doubly difficult for us to describe God and when the Church describes God we must keep in mind that she is talking in analogies to describe transcendent things.
As the Catechism says:
God transcends all creatures. We must therefore continually purify our language of everything in it that is limited, image-bound or imperfect, if we are not to confuse our image of God - "the inexpressible, the incomprehensible, the invisible, the ungraspable" - with our human representations.[1] Our human words always fall short of the mystery of God.Admittedly, in speaking about God like this, our language is using human modes of expression; nevertheless it really does attain to God himself, though unable to express him in his infinite simplicity. Likewise, we must recall that "between Creator and creature no similitude can be expressed without implying an even greater dissimilitude";[2] and that "concerning God, we cannot grasp what he is, but only what he is not, and how other beings stand in relation to him."[3]
Catechism of the Catholic Church.
[1] Liturgy of St. John Chrysostom, Anaphora.
[2] Lateran Council IV
[3] St. Thomas Aquinas, Summa Contra Gentiles I, 30.