The philosophical mindset of institutionalized science is that of absolute atheistic naturalistic materialism. It is fundamentally naturalistic because only naturalistic causes will be considered. It has almost become a determination to force naturalistic explanations on everything.
Inherently atheistic
It is atheistic because it fundamentally excludes God, as demonstrated by the reaction to intelligent design. It is fundamentally materialistic because only materialistic causes are considered. This is done despite Quantum Mechanical evidence to the contrary.
Problems with Materialism
Materialism has many problems, among them is where did all the material come from? However, there is an ultimate problem with materialism that causes problems for developing a real materialistic model of reality. That problem is that in order to work, materialism needs to have an ever-shrinking continuum of smaller size. This results from the fact that to produce the interactions that we observe, the particles that we know of and the fields that produce them would have to ultimately consist of smaller particles. Quantum Mechanics not only causes problems for this situation, but it goes against strict material determinism,
Abstract concepts such as consciousness, logic, math, information, and morality are fundamentally immaterial. The simple fact of the matter is that there are aspects of reality that are fundamentally immaterial. In fact, Quantum Mechanics makes more sense from the perspective that reality is fundamentally an information system rather than materialistic.
The interaction of field particles
To interact as needed, these particles would have to consist of even smaller particles, which interact using other particles. Ultimately, regardless of the model, there is no bottom to this process. You must have a continuum that gets smaller and smaller, reaching a point where it can never be tested.
Materialistic theories proposed for unification
Every materialistic theory proposed for the unification of the forces of nature ultimately suffers from this problem. This includes ideas such as string theory and M-theory. After all, those vibrating strings need to consist of something that is going to be flexible enough to vibrate, and this can only be smaller particles bound by other particles.
Problems with materialistic quantum mechanics
The problem is that Quantum Mechanics includes many clearly nonmaterial aspects. The Heisenberg uncertainty principle shows that particles do not have a definite location or momentum, both of which material particles must have. Particle wave mechanics, where particles exhibit both particle and wave-like behavior, is also contrary to materialism. Particle decay behaves probabilistically, depending upon quantum tunneling to work. Planck units suggest physical limits to spatial and temporal sizes, along with energy density. All of this suggests that reality is fundamentally information-based rather than materialistic,
Conclusion.
Materialism forces a continual downward continuation of a smaller and smaller scale with no ultimate reality beneath it. This is because for such a system to work, you need particles and interactions at smaller and smaller scales. This ultimately requires a highly complex, never-ending system to work.
