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I think that one of the most fundamental issues that arise from The Matrix is the fundamental question of how we know what we know. At the start of the film, Neo is depicted as one who knows, but also recognizes that there might be another level of truth or knowledge that transcends the reality in which he is immersed. This is the idea of a "splinter in the brain," something that Morpheus suggests that Neo will never be able to explore unless he takes his challenge of embracing what else can be possible. In this idea of "freeing one's mind," it is a statement that knowledge exists on a couple of levels. The first is the knowledge of "the matrix," the socially controlled and accepted levels to which knowledge can be understood and gleaned. This is a practical and a type of knowledge that is of use, ensuring that the practices and function of "the matrix" can continue and be sustained through others' shared understanding of knowledge. At the same time, another form of knowledge is what exists outside of "the matrix," an understanding of knowledge that there can be elements that transcend physical reality or what is perceived as physical reality. Enabling Neo, and in a sense the audience, to understand that there might be something outside of "the matrix" becomes one of the major epistemological, or knowledge based claims, of the film.
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