It is always important to distinguish between science and opinion. ID – or to be more accurate, inferring intelligent design – is a scientific process. It uses analytical mechanisms that are open to consideration – and refutation – by other scientists. It is provisional, reproducible and falsifiable – it is open to the possibility that an inference of design may be overturned if new evidence comes to light.
Evolutionists are keen to get ID proponents to say who they believe the intelligent designer is – because they think that if the ID proponents admit that they believe in God, this will somehow invalidate their arguments, by removing them from the realm of science and placing them in the realm of religion or philosophy. However, the process of concluding that design is present is independent of who or what the purported designer is. We know that Stonehenge was designed, even though we don't know who the designers were or what it was built for. The presuppositions of the proponents of ID certainly lie in the realm of opinion. But this does not affect the validity, or otherwise, of their scientific conclusions.
In many posts on this blog, I have ended up supporting an Intelligent Design argument. This I would understand to be a conclusion that is scientifically supportable and refutable – even though comparatively little effort has been expended by the opponents of ID to produce arguments in the mainstream of scientific debate that would refute it. Far more ink (real and digital) has been spilt trying to establish that ID is in fact part of creationism.
As an evangelical Christian, my own presupposition is that there is an infinite-personal God, who brought the universe into being and who continues to oversee it. From time to time (relating to the Privileged Planet and the development of language, for example - see the next post!), I have related the scientific conclusions of ID to my own worldview. Unlike inferences of design, I would not regard this as science, but opinion. This sort of analysis is, in the sense that it is built upon my own presuppositions (however reasonable and coherent I believe them to be!), "speculative" and not part of science.
Methodological naturalism – which I understand to be something along the lines of conducting science on the basis that there is no such thing as an external agent – and philosophical naturalism – the prior assumption that there is no external agent – are confused by many people in the evolutionist camp with science, or being necessary for the discipline of science. On a day-to-day basis for most of science, this isn't a problem. Designer or not, the universe behaves according to laws. It is possible to determine G, or the outcome of a reaction between two molecules, or what a hybrid of two species will look like independently of whether you believe that gravity, electromagnetism and DNA require intelligent agency.
However, the belief that there is nothing "outside the system" is not science – it is an opinion. In historical terms, it is probably even a minority opinion – most of the founders of modern science operated believing in "uniformity of natural causes within an open system" rather than a "closed system", and believed that not only God but also human reason are agencies that "transcend the system". To put it another way, pursuing science on the assumption that there is nothing "outside the system" doesn't prove that there is nothing outside the system.
Believers in a "closed system" – who pursue science based on methodological naturalism – need to understand that their own presuppositions are neither more nor less relevant than those scientists who believe in an "open system". A scientist who believes there is no God would be infuriated if he was told that his research was invalid because of his religious beliefs. It's hardly surprising that scientists who believe that there is a God find it profoundly frustrating when their beliefs are used to undermine the validity of their research. And (please note, Science, Scientific American, New Scientist, Nature, newspapers) it's pretty poor science journalism that can't see that science isn't bound by a particular philosophical perspective.