One issue that often arises is of religion and its relationship with empirical judgments and reason.  One may be surprised to discover this issue is not new or peculiar to our present time but has, in fact, confounded great minds since the inception of the Christian Church. Saint Augustine, Galileo and Rene Descartes are just some people who were convinced that empirical judgments should be given deference over religious traditions and scriptural interpretations within Christianity.  I am not at all trying to disprove religion, I am merely trying to open up the possibility that what we see around us is true; scriptures are not intended to deny nature and nature should not be used to deny the scriptures.
Galileo, a Christian defending his scientific opinions from the papal authority, wrote a letter in which he described his view on religion and its interaction with natural law. Galileo states his understanding of how God uses scripture and nature as his tools: “God reveals Himself no less excellently in the effects of nature than in the sacred words of Scripture … and so it seems that a natural phenomenon which is placed before our eyes by sense experience or proved by necessary demonstrations should not be called into question, let alone condemned, on account of scriptural passages whose words appear to have a different meaning.”
Since God has control over all revelation, the apparent discord is simply a product of misunderstanding which deserves to be heard out or disproven. Obviously, there is a good deal of weight put on the power of the mind and good evidence, but this too is part of Galileo’s conviction, that we are capable of making sense out of the universe; he says, “since [reason] too is a gift from God, one must apply it to the investigation of the true meanings of the Holy Writ at those places which apparently seem to read differently.”  Galileo thus sees reason as a lens for gaining insight rather than as a stumbling block to understanding doctrines.
Additionally, scriptures should not be read as a textbook on science because much of what was written was not trying to make claims about natural law. The original readers of the Old Testament were ex-slaves living in the deserts of the Middle East, the last thing they were concerned with was whether or not the Sun was at the center, how long creation took or any other issues that pop up from a literal reading of glossed-over physical descriptions of the world.  Galileo says the biblical authors were so unconcerned with making scientific claims that they avoided writing about them at all, “(they) deliberately refrained from doing it, even though they knew all these things well.”
Descartes’ explores our ability to have knowledge in his “Discourse on Method,” implicitly remarking on our understanding of truth in religious tradition.  Descartes had a low opinion of sense perception or appeals to authority because he acknowledges the ability for anyone to have wrong ideas that sound good or for our senses to be deceived by illusions; he says, “We should never allow ourselves to be persuaded except by the evidence of our reason.  And it is to be observed that I say ‘of our reason,’ and not ‘of our imagination’ or ‘of our senses.'”
Descartes himself formulated a large number of completely wrong scientific theories, but what counts is he endeavored to explain phenomena from natural law. 
He believed with God maintaining the universe through the same miraculous power that started it, utilizing natural law as a mechanism, the workings of the universe over time are open to our understanding and our use of scientific reasoning is useful for getting a better understanding of religion.
Galileo puts it eloquently when he urges us not to force scientific meanings on scripture, “I should think it would be very prudent not to allow anyone to commit and in any way oblige scriptural passages to have to maintain the truth of any physical conclusions whose contrary could ever be proved to us by the senses or demonstrative and necessary reasons.  Indeed, who wants the human mind put to death?”
Saint Augustine, early in the Christian Church’s history, determined reading literal meaning into scripture’s physical descriptions of the world was a bad idea.  To anyone who has difficulty believing the words of scripture because they differ from reality, Augustine wrote this in his book “The Literal Meaning of Genesis,” “Since the issue here is the authority of the Scripture… it should be said that our authors did know the truth about (the shape of heaven), but that the Spirit of God, which was speaking through them, did not want to teach men these things which are of no use to salvation.” 
Therefore, in addition to the impropriety of using scripture in a scientific debate, arguments should also not be made for the invalidity of the scriptures due to alleged scientific inaccuracies in the text or in a certain group’s interpretation.
From a biblical standpoint, religious views must be compatible with rational demonstrations because both come from God.  In the case of Christianity, the Holy Spirit’s revelations from scripture and from natural phenomena are not able to disagree except in their interpretation. 
Therefore, since reasoning is such a useful tool and has this use as a corrective lens, I would even urge people who have already made a judgment against religion to reconsider, to take the overarching message that is the real focus of the scriptures and examine what is really being said.