Reason, Religion, and Morality
Reason is a tool. You use it to accomplish goals, but the goals you have, at least the ultimate ones, do not come from reason. The need for food, for sex, for the admiration or our peers, for safety and comfort and health and love- these things all have rational reasons to exist in evolved beings, but as those beings, we do not choose them. They are us, and we simply act upon them. A mother does not love her child because she has reasoned out that it is a carrier of her genes and therefore represents the best chance for those genes to exist into the future, she loves her child because that love is a part of her being, it comes before reason. Therefore, all of our goals in this life are effectively irrational- not because they are wrong or stupid, but because they exist prior to our reason- they drive reason, and without them we would have nothing to be reasonable about.
This having been said, reason is still the very best tool we have for achieving our goals, and thus for being happy. It's like reason is a man driving a car and emotion is his pregnant and due wife in the back seat- every time she yells for him to go faster he feels a strong need to do so, but if he is in heavy traffic it's better for him to go slowly and avoid an accident. Reason allows us to put off some of our drives in order to fulfill all of them better in the long run. It is absolutely necessary to survive as a human being.
Religion is a thing of emotion. It capitalizes on every drive we have- the need for community, the fear of pain, it even tries to control our sexual behaviour so that only with religious sanction can it be satisfied. The problem comes in when religion makes truth statements- things about science, about morality, about race and sexuality and biology and family- statements not based in a reasoned understanding of the topic, but in a need to appeal as much as possible to the emotions. Religion allows us to abdicate our reason when it tells us uncomfortable things. Think gay sex is gross? Religion will tell you it's a sin, and viola, you're not a bad person for hating gays. Never mind that two guys doing it in the privacy of their own home can't possibly hurt you, and reason tells us that the 'lifestyle choice' explanation is highly flawed, as long as we have a bronze-age living manual that tells us it's bad, we can keep saying it's bad in good conscience. Except we can't.
Reason is necessary for morality. Morality must be based on mutual rules about behaviour between individuals. Those rules have to be equal, and have to be governed according to a rational principle, or they can't possibly function. This is because if you declare morality to be something based in emotion, it will always be biased. Some 20-year-old guy gets drunk and causes an accident, hurting your family, you'll bay for his blood, or at least a serious jail term and permanent suspension of his licence- but what if that 20-year-old is your brother or your son, you know he's a good kid, you know he can turn his life around if given a second chance- which side of this is right, if you go according to the emotions? Neither, both- there is no right answer, because both have validity, and a solution is impossible because there is no way to judge between the validity of each perspective. Only if you create and maintain a rational set of rules can a moral system or legal system or any other such thing function.
Religion, however, applies only to the emotions when it speaks of morality- 'do what I say or I’ll torture you forever' is typical, 'eye for an eye' competes with 'turn he other cheek', killing witches is out but shunning gays is ok. Religion allows people to ignore reason and still claim to be moral, but what it is really doing is denying the key component of morality- reason. Religion demands or at least allows for people to abdicate their reason. Without reason, morality is impossible. Therefore religion is not just morally bankrupt- it is necessarily immoral.