Choosing the right glasses
     In order to prove anything, we start with assumptions. If those assumptions are true, they will aid us in understanding the world, but if they are false, they will adversely affect our conclusions. Are all assumptions equally valid? Certainly not, but how do we test them? These are not physically derived concepts, which we could test empirically.
     We test our presuppositions logically. By logically, I mean that we see if they are consistent with themselves and each other. If an assumption contradicts itself, we discard it as a fallacy. If two assumptions within our worldview contradict each other, we discard one of them.
     There are two fallacies to keep in mind when refuting materialism. The first is the empiricist fallacy: the notion that all knowledge is derived empirically. As we noted, the assertion itself is not derived empirically. The second is the pretended neutrality fallacy: the notion that we can be presuppositionally neutral. This is sometimes known as “neutralism.” As we noted, all knowledge is derived using metaphysical assumptions.
     Both fallacies have something in common. In both cases, people claim to prove empirically what they assume from the start.
     The battle within science is not over finding the right facts. It is a philosophical battle over choosing the right “glasses,” the right worldview, the right paradigm. Good science is more than a pile of facts; it involves a proper perspective of the facts. 
     Facts are not the point of contention. We all have the same facts, the same data.  When I tap my fingers on the surface of a table, the reality of that experience is the same for me as it is for anyone else. A Christian and an atheist come to the same table and study exactly the same data.
     The difference is interpretation. Christians see order and purpose. Atheists see chance and chaos.
We cannot prove our worldview empirically, because it is the paradigm through which we interpret the facts. No matter how many facts we throw at it, the paradigm will interpret them to its favor. 
     Of course, naturalists say that we should throw away the glasses and simply look at the facts. Set aside all religion, philosophy, ideology, all metaphysical biases, and look at the facts. They presuppose (note irony here) that the facts can speak for themselves. 
     They don’t. All knowledge – including that of the facts themselves – is derived using assumptions. Science is natural philosophy. Scientists interpret facts within the context of their paradigm: their philosophical model.
See details: Bias