[Note: This is kind of a response to JohnJ's post "The Case Against Atheism," [201308031125 edit: this blog no longer exists. :'( ] in a "roundabout" way.]
Lately, I've been trying to figure out how to deal with life and my problems rationally, and recognize emotion when it arises within me and prevent it from interfering with logic. For example, a lot of people seem to confuse "common sense" with logic or rationality. This is a mistake. It's actually very easy to "fool" common sense (see: the Monty Hall problem).
Another all-too-common mistake is "looking through the wrong end of the telescope." For example, I assume (and I'm sure that JohnJ does as well) that there is an "objective reality" that's observer-independent. The reason I assume this is that the universe existed before there were any observers (I'm sure JohnJ has his own reasons). I often make the analogy that this "objective reality" is like a picture. But it's obvious to me that the only way available to us to see "the big picture" is through science/reason: one "puzzle-piece" at a time. One of the positive aspects of this is that there are correction mechanisms, for example, if the pieces don't all fit together, then that's an indication that someone has made a mistake. I don't believe that anyone has or will show us "the big picture," so we have to try to piece it together ourselves.
It seems problematic to me that throughout history, people have claimed to have access to a "full" or at least "better" view of this "picture" through some other means than discovering it for themselves in verifiable ways. The claims of these people have often been shown to be false—earth is not the center of the universe, nor is it flat, nor is it sitting atop the backs of turtles or elephants or whatever—and don't even get me started on "mind-body dualism." [Personally], I'd be at least a bit reluctant to believe anything I was told about the missing parts of the puzzle by those who have been (continually) demonstrated to be incorrect regarding the pieces we do have.
Another way of "looking through the wrong end of the telescope" is to assume that the "law" governing the universe is some kind of "intention," i.e., to assume that things happen because they were "meant" to happen. The only "laws" governing the universe are the laws of physics, the fundamental forces, [blah, blah, blah...] I wonder, if the leaves on a tree could "think," if they would think that their existence was the "purpose" for the existence of the tree to which they were attached, or the existence of trees in general. I'm sure that the "odds" of any specific leaf appearing at any specific place on a tree are quite small. But probability isn't the "law" that governs the universe, either. The "law" is cause and effect (and let's throw some "quantum mechanics" in there "for good measure"). The interactions are just too complex for us [given current technology] to predict with absolute certainty what will happen next, so probability is a heuristic we've developed to help us achieve at least some degree of certainty.