It's the division of two areas of reality, saying that there is more than one way of knowing. For religion, I go to my bible, for the empirical world, I go to my micro/tele/stethoscope. This compartmentalization of critical thinking happens in more places than the classroom and outside class, religion and science, but I'm going to stick with these two examples for now. I am arguing that what you learn in biology about evolution isn't just true on the test, it's true in the rest of the world. What you learn in sociology about race and class inequality isn't just a simple topic for your paper, it's based on facts about the reality that we live in. But most of us shut down these systems when we pack up and go home for the summer, the weekend, or even just tonight for this party. Nothing kills a person's buzz quite like reminding them that they're wrong, despite the fact that they learned the right answer."...we get the age of rocks, and religion retains the rock of ages; we study how the heavens go, and they determine how to go to heaven."
This does not happen to everyone, but it happens to enough people for it to be concerning. It is the explanation for how we have wonderful scientists such as Dr. Francis Collins, the head of the NIH, who happens to be a devout Christian. He keeps his religion and science separate. He doesn't tell his colleagues not to run tests, but rather to pray. He does not attribute the success of the treatments at the NIH to God's will (at least, publicly). So why is there a problem? He is still compartmentalizing his critical thinking. He is using it in one area of his life (his work) and not applying it in others (his personal).
To get an idea what I'm talking about, think about a very simple concept that is basic to all religions: prayer. The idea that someone who does science for a living could at the same time believe in prayer is a complete division of reality within the mind of that individual. The issue with prayer is that it has zero verifiability. If it did, if it worked with the certainty you might expect from such a popular activity, then we could just fucking pray away world hunger, racism, and give each of us a million-dollar mansion to live in. Prayer seems to only give us things that could have happened in the absence of prayer. In fact, whenever we attempt to measure the effect of prayer, we have either found no effect, or (ironically) the opposite effect.
Critical thinking isn't always easy, but you actually do it more than you might know. Imagine this scenario: you attempt to turn on your TV with the remote and yet nothing happens when you press the "on" button. The first thing to pop into your head is probably not something along the lines of "god is punishing me" or "evil demons have destroyed my tv." No, you're probably (no matter how religious you are) bound to come up with a physical, natural explanation. The batteries in the remote might be dead, so you switch them from your DVD remote and see if they work. They don't, so you switch them back into the DVD remote to make sure THOSE aren't dead either. When in the DVD remote, they work fine, so it's not the batteries. You attempt to turn the TV on with the power switch on the front but nothing happens. You think the TV itself may have died, but there are other things to check first. You look behind the TV and notice that the plug had merely come out of the socket. You plug it back in and the world as you know it returns.
We have all probably done something like this before. And guess what? You were doing science! You (very quickly) created hypotheses and tested them, looking for results. Why is it easy to think critically in this situation and not others? The easy answer is that the results are instant. With the concept of prayer, you have to wait. And when you have to wait for as long as you do, such as for God to send you a husband, or for your depression to go away, or to get a promotion at your job, then you really have no way of telling if it worked. But, you may remember that you prayed about it. And when you credit prayer, you ignore the fact that you may have done hard work and earned the promotion, that serendipitous circumstance led you to your latest love, or that the medication you're taking is actually responsible for your good mood. In this sense, prayer is antithetical to understanding our world, because it robs us of actual explanations.
So whenever I hear someone say, "Stop making me think!" because I am pointing out their inconsistencies, it makes me sad. It could be that they're a biblical literalist and yet they claim to support gay rights - you can't have it both ways. Or when someone writes that they "don't trust science" from a computer whose technology could not have been built without thousands of scientists doing their job every day. Or when my friends with PhD's--whose job it is to think critically--tell me that they see psychics.
I'm not going to stop making you think, because I believe it is the most important thing you can do.

