Science The empirical sciences
Science has long been celebrated as an enterprise entirely immune to the subjectivity which pervades such disciplines as religion and moral philosophy. The frequently perpetuated cultural stereotype is that science provides a methodology that objectively filters out distortions which are impressed on the data by ones personal worldview commitment or a priori ideology.
Such a view of science has gained widespread popularity because of a blending together in the publics understanding of what are essentially two fundamentally different types of scientific enquiry.
What allows scientific theories such as the germ theory of disease, Mendels theory of heredity, Newtons laws of motion, and Einsteins theory of general relativity, to be empirically verified in a way in which certain other types of theories are not? All of the aforementioned theories, of course, are theories about the way in which natural phenomena operate in the present. Such theories can be checked by determining whether it corresponds to reality. In other words, empirical science, which encompasses all the above, can be verified by making a comparison with the way natural phenomena are actually observed to behave.
The possibility of such empirical verification is why the scientific methodology is widely celebrated as a worldview-neutral enterprise, completely devoid of theological or philosophical commitment. Scientific theories, as far as the empirical sciences are concerned, deals with repeatable observation.
Science The historical sciences
Besides the empirical sciences, which concern the operation of natural phenomena in the present, there is also the enquiry of the historical sciences. Unlike the empirical theories which focus on things occurring in the present, historical theories focus on singular events in the past. When scientists attempt to identify the most causally adequate explanation for an event in the remote past, they invoke the cause known to produce the effect in question. For example, if one wants to explain the presence of volcanic ash, one does not invoke an earthquake, because earthquakes have never been observed to produce volcanic ash, whereas volcanic eruptions have been. This makes the volcanic-eruption-hypothesis the most causally adequate explanation of the presence of the volcanic ash in question.
When it comes to explaining certain types of patterns that appear in nature, we have different categories of explanation. Nobody would think to attribute the inscriptions on the Rosetta stone, or the carvings on Mount Rushmore, to wind and erosion. Wind and erosion have never been observed to be able to produce the effects in question. Such patterns exhibit features which are best attributed to intelligent, not naturalistic, causation.
This methodology, of course, becomes somewhat more controversial when one is dealing with biological systems. Why? From a reductionist perspective, the phenomena described above require nothing more than the invocation of an evolved intelligence. For biological systems to have been designed, it would require an unevolved intelligence. This eventually boils down to a fundamental conflict between two opposing views -- theism and reductionism. Nonetheless, the cell has been demonstrated to exhibit large volumes of specified irregularity (a synonym for information). Law-like, material mechanisms have never been demonstrated to possess the causal capacity to account for such levels of specified irregularity. In our uniform and repeated experience, we know of one and only one cause, which has been demonstrated to be causally adequate to produce the effect in question, and that is intelligence.
Science Theology: Friend or Foe?
Science can ultimately determine certain facts which can inform theological disciplines. It can determine, for example, that the universe began to exist at some point in the finite past. It can determine that certain features of living systems were likely the product of intelligent agency. Nonetheless, questions relating to the identity and nature of that intelligent agent are secondary questions, and enquiries better suited to such disciplines as philosophy and theology.
Theology is ultimately concerned with ontology -- to whom, or to what, does the universe owe its existence? Questions relating to ontology, therefore, are not matters of scientific enquiry. The scientific methodology presupposes uniformity in the fundamental physical laws and constants. It can thus not answer questions pertaining to their origin without reasoning in a circle.
In conclusion, theology and science -- though related -- are fundamentally two types of enquiry. While one can certainly inform the other, one may not be misused to trump the other.