[FeepingCreature]

There are views where there is an implicit substrate that exists in another layer of reality, ie. dualism. That layer is generally not counted among the substrate. So a computation can be substrate dependent by introducing a non-material cause. (Disclaimer: I don't personally know anyone who believes anything like this, so this may be a bad paraphrasing.)

[mistermann]

If the computation doesn't compute completely and deterministically on all substrates, then it isn't substrate independent though is it?

Human cognition would be a good example of substrate dependent computation I'd think....it even varies per instance of substrate.