Misusing philosophy and logic

Philosophy and logic are tools. When properly used, they can be beneficial and useful to create the guiding principles of science and inquiry, in order to minimize and avoid mistakes and errors in methodology. They can help spot defects, flaws and shortcomings in the way in which things are investigated, observed and tested, and how the test results are interpreted. For example, they can help avoid common mistakes such as deductive fallacies and biases. They also help making it clearer what the limits of the investigation are (in other words, so that the experimenters don't jump to conclusions without sufficient justification.)

Without philosophy and logic, science would be much harder and error-prone. However, philosophy and logic all by themselves cannot be used to discern and establish how the universe works and what's real and what isn't.

The reason for this is that they always start from certain assumptions. These assumptions have to be based on actual observation and evidence, or else the reasoning will be flawed. Also, more often than not there tend to be hidden assumptions that might not be stated explicitly, but are assumed to exist (for example that there's nothing else affecting the outcome of the chain of logic.)

Logical deductions can be used to make predictions. Sometimes these predictions are correct, but sometimes they aren't. In the latter case it doesn't necessarily mean that the logic was incorrect. It may simply be that either the initial assumptions were too simplistic, or that not everything was taken into account (that is, the hidden assumption was made that nothing else affects the end result.)

Thus logical deductions should always be corroborated with actual physical observation, measurements and experimentation. Until this is done the deduction cannot be established as being true. (History is full of examples of incorrect predictions that may have been logical, but were based on incorrect or flawed premises.)

Many Christian apologists try to argue that philosophy and logic is enough to establish what's real and what isn't. They want to make logical deductions and bypass the physical corroboration part, and proclaim their argument to be a well-established fact based solely on philosophical grounds.

William Lane Craig is one of the best possible examples of this (although he is by far not the only one.) He actually explicitly makes the argument that philosophy is enough all in itself to establish what's real and what isn't. (He also shows an incredible amount of smugness and douchery in this category in that he likes to belittle his opponents if they don't have an "education in philosophy", making them incapable of fully understanding his arguments. As if philosophy were some kind of higher form of science.)

All these apologists always make the same two mistakes, both of which are quite egregious:

1. They always start from unjustified premises, assuming their veracity from the get-go. (This often takes the form of what I like to call "removing the conditional." This means that when in propositional logic an argument typically has the form "if X, then Y", the apologists just outright assume X, and state it as "X, therefore Y." The assumption is often completely unjustified.)
2. After the proposed chain of logic, they always make huge leaps of deduction. (This typically takes the form "...therefore X. Let's label this X 'God'. That's the God of the Bible, of course." This is done without even a semblance of justification.)

They also typically make all other kinds of mistakes and hidden assumptions (such as assuming that nothing else affects the end result.)

However, in the end, the major mistake is that they assume that philosophy and logic on their own can be used to discern reality. They think that if they come up with a logical-enough chain of deductions, that settles it. No actual corroborating experimentation is needed. This has never worked, and never will. We do not discern what's real and what isn't by playing with words. We do it by observing reality. Words can be used to make predictions, but they cannot be used to establish reality.