In his famous book "The Structure of Scientific Revolutions," Thomas Kuhn explained how empirical data is interpreted through pre-empirical assumptions about how the world works and how explanations should look. He analyzed the change from an Aristotelian framework to the Copernican framework.
Currently, the "hard sciences" tend to ignore his work, and the social sciences often claim that Kuhn's work proves all is relative. By way of contrast, I believe he helped identify how interpretation works, and at the very least pointed us in the direction of identifying contemporary pre-empirical assumptions that are taken as "hard fact."
Simply stated, Kuhn argued that a paradigm is in place that tells the scientific community what an acceptable interpretation of the world looks like. In the Medieval Age this was Aristotle's understanding of potentiality/actuality, the four causes, and the eternal circular motion of the planets, sun and stars around the earth. The change brought about by thinkers like Copernicus, Galileo, and Kepler was not due to more empirical data. What Kuhn called "anomalies" already existed. Anomalies are empirical data that is contrary to the existing paradigm. The reigning thinkers ignore these. However, as they build they provide alternative systems an opportunity to suggest another interpretation.
What caused the change from the Aristotelian system to the Copernicus/Galileo/Kepler system was a change in belief about causation and eternal being. These later thinkers, notably Kepler, argued that the sun was created by God and therefore not in eternal (beginning-less) motion. This is not an empirical observation, but the diference between Greek Dualism and Christian Theism. The Medieval Age saw numerous attempts by Christians to wed Greek Dualism with Christian Theism, and the scientific revolution was a move toward greater consistency as these were separated.
I believe we can apply these insights to our current age. The paradigm that has reigned since the 19th century is called naturalism. Naturalism argues that only material causes can be used to explain the universe as we now see it (in contrast to Aristotle's 4 causes, and in contrast to Theism and God as a cause). Like Aristotelianism, this is a paradigm that is pre-empirical. The empirical sciences are limited to measuring the material world, and therefore the empirical sciences cannot disvoer that only the material world exists without begging the question (circular reasoning).
Uniformity is the belief that the world as we now see it was formed by physical causes currently seen operating and at the same magnitude observed today. Therefore, when considering how the surface of the earth was formed, current weather patterns are projected into the past to get large amounts of time; when considering how the earth and solar system were formed, current changes in the system are projected backwards in time to get significant amounts of time; when considering how stars and galaxies were formed, currently observable changes are projected backwards. The same is true in accounting for the universe itself.
Common examples of this are "dating mechanisms" that rely on the half-life of a particle like Carbon 14 or Uranian 236. Measuring the current amount of the particle in a bone or rock, and knowing the half-life decay of the particle (the number of years it takes for the amount to decay in half), and assuming the original amount, an easy equation can be used to argue about the age of a bone or rock. However, there are two naturalistic assumptions operating: that we know the original amount, and that the decay has occurred as is now observed. Changes in either of these dramatically change the equation.
The naturalism of the 19th century became the controlling paradigms for a number of reasons, including that appeals to non-material causes appear arbitrary, it offered unity in a worldview in contrast to the great divisions in theism, and it boasted technological advances.
It is true that if appeals to non-material causes are required there must be a non-arbitrary way to do this. Similarly, divisions among theists are disastrous if theism, and Christianity more specifically, is to be taken seriously. The claim that naturalism has given the world technology is far from true in that the basis for technological advances came from thinkers during the early part of the scientific revolution who were motivated by Christian theism and sought to understand the world in order to understand God.
There are significant anomalies building up against naturalism. As Kuhn predicted, naturalists generally ignore these. However, the paradigm itself is open to change as it is seen that naturalism and uniformity are not empirical conclusions, but rather are philosophical assumptions used to limit how data can be interpreted.
I'd like to conclude by suggesting a few areas where naturalism has shaped the interpretation of empirical data, and this interpretation has become the reigning model of "scientific knowledge." These are the origin of the material universe, the formation of the sun and stars, the formation of earth, the geological and geographical features of the earth, the origin of life, the origin of species, and the origin of humanity and human civilization. Finally, I'd like to point out that naturalism takes for granted that there has always been natural evil (old age, sickness, death, toil, strife, famine, war, plague). Naturalism says that natural evil is "just how the world is." This, of course, cannot be discovered empirically, but is an assumption.
By way of contrast, if God created the world very good then there has not always been natural evil. The change from no natural evil to natural evil is a change in the world that cannot be accounted for through material causes. This is a central example of how naturalism and theism differ in their understanding and interpretation of the world.