Those who know me as a scientist and are interested in picking a fight with me (especially religious people who might consider scientific knowledge at odds with their belief system) are sorely disappointed when they discover just how accepting I can be of their views. Although I have a great love of science and see it as an extremely useful method for acquiring knowledge, I do not follow it religiously or seek to force a scientific explanation for things which are fundamentally non-scientific.
Scientific truth is not absolute truth. Science concerns itself primarily with what is empirical. What we can test empirically though so often comes down to what we can observe and this can sometimes be limiting. A theory can reach beyond what is directly observable and still be considered scientific, but it is only considered such because it best explains the observed phenomena.
As an example of something that is scientifically true but was not thought to be so at one point, let's consider the electromagnetic waves that lie in spectra beyond what we can see. These waves (like microwaves and radio) existed before technology advanced to the point where they were empirically provable, but they were not considered a scientific reality until they entered the realm of empiricism. That does not mean electromagnet waves outside of the visual spectra did not exist, they were just not a scientific reality at the time. From past experiences like this we can speculate that there are, today, many elements of our reality which are not scientifically verifiable but may be brought to scientific light in the future. I am also willing to suggest that there are things in our reality which are indeed true, but may never be scientifically verifiable (Now this is a stance that really gets me into trouble with my scientifically minded friends!).
Science, limited by our powers of observation, is limited in what truths it can divulge. Science, therefore, is not an arbiter of absolute truth. Rather, science is an eloquent tool which enables us to make predictions which are largely accurate and advance technologically. It is a practical method of inquiry, but it is not always the best method, and I refuse to fully dismiss all other methods.
So what then is truth and how can one determine reality? Truth, in my opinion, is dependent upon the lens through which you are viewing reality. There is no absolute truth, and there does not need to be. Instead, veracity must be examined in the context of the conjecture.
Take for example, a discussion I had the other night regarding the possible past existence of dragons. From behind the lens of paleontology, dragons did not exist as there is no adequate fossil evidence. From the view of physiology and developmental biology, the proposed bodily design of many dragons is considered impossible and therefore they could not have existed. It is not until we consider the existence of dragons from behind the lens of anthropology and myth that they become real, as cultures across the world show depictions of dragons in some form or another in their written history. So did dragons exist? Yes and no. It depends entirely upon which set of philosophical spectacles you adorn.
Even more weighty questions involving such unearthly things as say, the meaning of life or the soul, are largely not only unexplainable by science, but not at all the concern of science. Enter religion, spirituality, and metaphysics. The fundamentally unobservable and untestable belong to their realm, and here I relinquish the driver's seat.