For half a century, the computer has been a dominant metaphor for understanding the operations of the brain. Even Descartes and Leibniz had intuited the potential of mechanism for understanding mental processing. Drawing on computational metaphors, representational theories of mind attempt to explore the organism’s role in cognition. The computer programmer can thereby put herself in the organism’s shoes. More recently, computation has served to understand the operations of the physical world at large. The computational metaphor thus reflects the development of technology—and the mechanist metaphor—from simpler mechanical systems to computers. The laws of physics are now regarded by some as computer algorithms and the hardware of the universe as a computer. The underlying metaphysical premise tacitly remains the same: nature is equivalent to an artifact, a machine, a text, a program, a product of definition. To qualify as a scientific hypothesis, such an assumption would have to be experimentally testable. It does not have to be tested, however—let alone be proven—to qualify as the basis for research programs. But, whether applied to the cosmos or to the brain, the computer metaphor continues to ignore the most obvious fact of physical reality, which is that it is not programmed by some external intelligence, but is somehow self-programming and self-activating. It is not an artifact, a product of our definitions (nor of the gods’). We may be deluded by our abilities to create convincing simulations. But reality and simulation are distinct things. One is found, the other made. Nature itself and our scientific models of it are also distinct things. Computer animation can be entertaining, especially when we indulge the illusion that it is real. Similarly, scientific modeling can be fruitful for specific purposes, which tempts us to think it provides an image of the world as it “really” is.