There are faults to ontological reductionism(I nabbed the term from Massimo's blog), but I would check the arguments made for causal completeness before asserting that dark matter mean's it's "all wrong". How many various explanations do you think we could come up with for what dark matter is? It's a great exercise for science fiction plotting, I'd think.It got me thinking about how reductionists claim everything ultimatley reduces to physics.
But what if our understanding of what is supposed to be the root of all explanation is wobbly?
Will the discovery turn out to be an entirely different set of atomic elements, made up of anti-matter and anti-energy? Or could there be even more than two full charts of a "type" of matter? Perhaps the answer is more mundane, perhaps an element we've not yet discovered exhibits properties we could never have predicted(an emergent property, if you will).
Perhaps the paradigm that will resolve dark matter is linked to the issue in harmonizing macro and micro physics. Or a revised understanding of Einstein's work.
It's fun to consider the possibilities. What would your idea be? Or do you think the matter of dark energy is forever insoluble? I think there's an explanation, seeing that the universe has had a history of reveals that match this very pattern. I'm not sure how long it will take, but we'll someday understand it. Then the home of god will move back another gap, as it always has.