You should never assume that humanity is at a state today to comprehend all that we observe.
Perhaps not, in the same way that the earliest scientists could not begin to mathematically probe the mysteries of black holes or the chemical composition of stars through analyzing their unique spectra. However, we can make observations and we can draw meaningful conclusions from those observations. If further evidences are discovered later which make those conclusions obsolete, then new conclusions accounting for the new evidence must be made and the obsolete ones discarded.
There may be things that we can not yet observe or confirm via experimentation as well as things that we can observe but are not yet technologically advanced enough to comprehend.
Perhaps spirits or the supernatural would fall under this umbrella. Science is designed to study the natural world, or if you prefer, the physical creation itself. It always seeks explanations within physical reality and does not reach beyond it. Science and religion are compatible, but they address different questions. Science may tell us how human beings came to be, but religion tells us what it means to be human.
It does not necessarily mean that G-d is trying to fool us or that science should come to a screeching halt. If anything, it means that we need to advance science further to understand certain things.
Exactly. If there were no unanswered questions, then we wouldn't need science anyway. Things that scientists do not know yet are good things, they allow us to continue to study and press forward and learn more.
My point was that if the universe is a big lie, or that if it was created to look like it was one age when it's really another, then we can't trust any of our observations.
Example:
You take a ruler out and measure an earthworm, and the earthworm is 5 inches long according to the ruler. Several of your friends use their own rulers, and come to the same conclusion. The earthworm is 5 inches long.
Then some religious person comes along and says "My holy book says earthworms never grow beyond 1 inch. If you're measuring 5 inches, then earthworms must have been created to appear to be 5 inches long in order to test our faith."
That sounds a bit silly right?
That's why I think the "appearance of age" doctrines are so silly.