You are right; my example was a bad one, and it does not support the point that I thought it supported. The mere fact that something takes unreasonably long to calculate does not mean that it is not an informative endeavour. (I may have been working from a bad definition of reductionism).

If you can demonstrate to me that there is some organizational structure of matter which causes that matter to behave differently from what would be predicted by just looking at the matter in question without considering its organization

Um. I suspect that this may have been poorly phrased. If I have a lump of carbon, quite a bit of water, and a number of other elements, and I just throw them together in a pile, they're unlikely to do much - there may be a bit of fizzing, some parts might dissolve in the water, but that's about it. Yet if I reorganise the same matter into a human, I have an organisation of matter that is able to enter into a debate about reductionism; which I don't think can be predicted by looking at the individual chemical elements alone.

But that behaviour might still be predictable from looking at the matter, organised in that way, at its most basic level of perspective (given sufficient computing resources). Hence, I suspect that it is not a counter-example.