The claim that the new science does not require a commitment to materialism can actually be broken down into two further claims: (1) The observations, predictions, and descriptions that empirical scientists have been making are perfectly compatible with the idealist view and, (2) The claim of these scientists to be discovering the microstructures that explain macroscopic phenomena are also consistent with idealism. We have already seen how Berkeley backs up these two claims: he asserts that what the scientists are discovering in both cases, are relations, or patterns, among ideas. The scientist observes connections among actual ideas, and makes predictions about future ideas. Since the connection among ideas are lawlike (that is, they constantly hold true), they allow us to predict with regularity what ideas we would have if we were presented with certain other ideas (for instance, that if we were presented with the idea "quickly moving particles" we would also be presented with the idea "heat"). When the scientist looks in a microscope he is observing some very particular sorts of ideas. God has set things up so that there are certain of our ideas that make up micromechanisms, in terms of which macrophenomena can be mechanically explained. Observing these micromechanisms provides us with a whole new law-like system of connections and regularities that we can use in order to predict and control the natural world.
Berkeley goes on to explain why this idealist interpretation of the new science is actually superior to the materialist interpretation. First of all, as he has already shown, materialism leads to skepticism. By claiming that there is some real essence in objects (i.e. some internal qualities or constitution) that is hidden from our view, the materialist interpretation implies that there is a limit to our knowledge. According to this view, we cannot comprehend everything there is to comprehend about the natural world. Locke himself showed where this limit comes in: we cannot understand how the internal constitution of objects gives rise to the secondary sensible qualities we observe, such as color, taste, smell, and sound.
The materialist interpretation is needlessly complex. By including matter in the picture, it adds an element that can do no explanatory work for us. Matter is by its nature something that transcends our experience (since all we experience are sensible qualities, and these cannot belong to matter), but what we have to explain in science is the behavior of the objects of our experience. Matter, then, cannot help us to understand the world any better.
Hylas is satisfied with this two-part response to the challenge from science, but should he be? Many problems still remain with Berkeley's account. First of all, Berkeley's interpretation seems to discount the importance of scientific truth. We do not just want our theories to make accurate predictions; we want our theories to identify the real causes of the phenomena we observe. We want our theories, in other words, to describe the way the world really works. But on Berkeley's view, our scientific theories cannot do that. The way the world really works, according to his idealism, is that God controls all of our ideas according to certain rules. We might be able to figure out these rules well enough to predict which ideas will follow which others, but we will never understand the reasons for these rules, and we will never really understand how and why our ideas are produced in the order and manner in which they are. Science will always only get us as far as our own ideas, and never to the controlling God behind them, and so it will never tell us how the world really is.
We also believe in scientific truth when it comes to the microscopic level. We think that when we discover how the microstructures of objects are organized, we are getting at the inner workings of things; we do not think that we are just adding more ideas to the mix. We think that the microstructures are actually a part of the macroscopic object, not just further ideas that are somehow correlated with that object in our experience.
Given that Berkeley thinks that microstructures are simply further ideas, we might even ask why he thinks they exist. Why would God even make these ideas of molecules and atoms? These microscopic ideas, which must then be correlated with the macroscopic ideas, just needlessly complicate the world. Why would God not make the world simpler, so that we could just look and see the laws of nature are with our bare eyes? Berkeley tells us that these microscopic things exist because God thought it would be best for them to eixst, but this is no explanation, just an assertion.