There is a strong difference between science and the humanities, including disciplines such as philosophy and theology. Those who follow scientism (the belief that science alone is the highest human discipline) often seem to be very confused about how science cannot study, research, analyze, and then from that explain the who, what, when, where, and why of all of the physical world.
A great example, ironically from the atheist camp, illustrates this point. In his book The Gospel of the Flying Spaghetti Monster, Bobby Henderson explains how global warming is a result of the decrease of the number of pirates on the planet. He argues that because global temperatures have increased and the number of pirates have decreased over the same period of time, then they must have a causal relationship; viz. one made the other one happen.
Did you spot the major flaw in that argument? How could it be even likely that fewer pirates have had that sort of impact? Science can only show that global temperatures have gone up and the number of pirates have declined. Science ends with the collection and presentation of data. After that comes the need for chin-scratching, question-asking, and theory-creating. Henderson comically leaps to the conclusion that these two pieces of data must be related, and therefore the solution is to recruit more people to become gold-hungry buccaneers in order to save the planet.
Dead Pastor's Society 