Many people see philosophy and science as two mutually exclusive things, however they are two topics that are heavily intertwined. In Plato's "Allegory of a Cave", from Republic, he covers this scenario where truth is purposefully hidden from man, and that what we see isn't truth, but rather a shadow of truth. In the allegory, Plato describes a group of people chained inside of a cave, completely immobilized, and facing the wall of the cave. Behind them is a fire that illuminates passers-by and casts a shadow upon the wall that the prisoners of the cave are facing. Eventually the people will come to associate the shadows cast with the actual objects. If the prisoners were released from the cave, they wouldn't be able to cope with seeing the true object that was casting the shadow. At first they would only identify the objects by their shadows. Eventually however they would be able to understand that what they had understood for so long was a shadow of truth.
Plato used this allegory to show how humanity would react if the facade was removed and man was shown truth, in its most absolute and perfect form. The point was that our methods of observations are inherently flawed, and can only tell us so much about the universe, because since we are still inside "the cave" (in this case the cave being the system in which all things exist, the Universe) and not removed from it we are unable to understand and grasp absolute truth.
Modern science, especially when in the terms of quantum mechanics, particle physics, and string theory, show us that there is no such thing as objective reality. Time and space are both subjective by nature, and this throws a huge wrench into the plan to use them as an objective base to build hypotheses and theorems upon their backs. It seems the smaller we get into the atom, and we begin to branch off into quarks, muons, and bosons, the less we actually know about the universe, and the more unstable our previous theories look. Like an infinite regression of a gobstopper, each layer we peel back reveals only another layer.
"to be is to be perceived." - George Berkley
links:
Plato's "Allegory of a Cave"
- http://www.historyguide.org/intellect/allegory.html
"Allegory of a Cave" Picture Explanation
- http://www.age-of-the-sage.org/greek/philosopher/platos_cave_the_republic.jpg
Quantum Mechanics and Reality
- http://www.integralscience.org/sacredscience/SS_quantum.html