Yes, of course they can, because after all we create theories, and we're computers - but this is less trivial, because this is the first time silicon computers have created theories. There have already been exercises where data about the motions of bodies in the Solar System was put through automated inductive reasoning and reproduced the laws of gravitation. But this is different, because we already knew the answer when we re-constructed laws of gravitation. Software has now solved a problem in genetics that troubled the field for a century. (Original paper here.)
An objection might be "but does the computer understand the theory?" We humans often have a non-propositional, subjective sense that we understand something once we arrive at a model. But this sense is really like an emotion - that is, an internal experience that doesn't correlate to an object in the external world, and is separable from the reality it purports to relate to. That is to say: everyone has had the experience of feeling a "Eureka!" and then realizing they were wrong (and this feeling can range from seconds to years) - just as people with panic disorder genuinely feel terror as if they're going to die when they have a panic attack, without actually having their lives in jeopardy, in a kind of emotional hallucination. The computer is likely not experiencing a subjective eureka, but this has nothing to do with being correct.