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. 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.
Materialism has many problems, among them is where all this material comes from. However, there is an ultimate problem with materialism that causes problems for developing a real materialistic model of reality. That problem is that to work materialism needs to have an ever-shrinking continuum of smaller size. This results from the fact that to produce the interactions we observe and the particles we know of and the fields that produce them would have to consist of smaller particles ultimately.
To interact as needed these particles would have to consist of even smaller particles that interact using other particles. Ultimately, regardless of the model, there is no bottom to this process. You must have a continuum that just gets smaller and smaller reaching a point where it can never be tested. Every materialistic theory proposed for the unification of the forces of nature ultimately suffered 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.
In conclusion, materialism forces a continual downward continuum of a smaller and smaller scale with no ultimate reality beneath it. This is because in order for such a system to work you need particles and interactions at smaller and smaller scales. This all ultimately requires a highly complex never-ending system in order to work.
