Philosophy of science, like any other area, struggles with both method and framework. The methods side of the equation is most familiar to us. These are the questions of how theories are best constructed. That is where I have spent most of my time. The challenges are significant for producing theories, whether models or empirical structures, which may be both falsifiable/verifiable and broad enough to encompass all available data. That makes for strong science.
The framework question is another matter. This question goes to the presuppositions and assumptions behind one’s theory. The most common of these are the ever-popular discussions of theism vs naturalism, metaphysical naturalism, and methodological naturalism. These are hot topics today especially in light of both the ID movement and the third way of evolutionary theory. Both of these acknowledge real data in the genetic structure (which Darwinists generally do not) yet fail to account for it. There are other assumptions which lead to further discussions on other matters.
One ever-popular book in philosophy of science is Thomas Kuhn’s The Structure of Scientific Revolutions. This book remains a standard for many in the examination of how science develops. It is here that I think we would do well to examine Kuhn’s framework for history. It is here that we understand how he developed his understanding, for it did not occur in a vacuum. All people’s views proceed out of one’s worldview, one’s framework for understanding the world around us. Kuhn is no exception.
Kuhn’s perspective is that science develops and progresses through conflict and resolution. First the myths of a people are blurred (p. 84). Disarray ensues. But the vacuum cannot remain for very long. New theories are developed to fill the gap left by the old myth. One example of this noted by Kuhn is the mechanics of Newton. For the most part it works. But out on the fringes it does not work. The more the evidence on the edges piled up the more the mechanics of Newton were rejected. Einstein filled that gap with his new theories.
What was “fact” with Newton became “myth” as exceptions piled up. Though a model or theory may not be immediately rejected based on exceptions, it may be rejected when so many exceptions pile up that the theory becomes broadly and generally unworkable.
Kuhn’s ideas bear some merit. He correctly identifies the mindset that refuses to dismiss a theory set because of its exception-handling issues (77 ff). He also builds a strong case that scientists need to account better for exceptions (he uses the terms anomaly and counter-instance) rather than going ahead with something that is known to be broken.
Yet one cannot read this work without picking up hints of something more significant. What are we to think of a cyclical worldview, one where process occurs not because of ideas but because of conflict? His is a worldview where ideas are not part of the mind. Rather the material world around us, nations and kingdoms, events and conditions, spark our ideas. It is a materialistic worldview. It is there that I believe his work falters.
For those interested, James Burke’s series, The Day the Universe Changed, comes with the assumption that it is ideas which move history along. This approach accounts for the mind, something which naturalistic evolutionary theory, at least the Darwinist camp, is not capable of accomplishing at this point in time. Like Burke it is my contention that ideas drive history. Teachers promote ideas and pass these on to their disciples/students. Whether Jesus, Mohammed, or Marx, these ideas bring their own results, their own consequences. Kuhn began with a presupposition, an idea. Conflict came later.
 References here are to the Second Edition, Enlarged, University of Chicago Press (Chicago) 1970.