@Fountofwisdom,
The question of "tools" is an epistemological one...i.e. we must examine the essence of "explanation". At present, what constitutes a
satisfactory explanation is couched in terms of "sucessful"prediction and control. But writers like Capra point out that such a "controlling" trait is a chauvinistic attribute of human "cognition". He points to alternative concepts such " life as a system" and to the mathematics of the
sustainabilty of such a system. This is an attempt at a non-anthropocentric approach in which "cognition" is relegated is a less important place in the system hierarchy.
Capra's approach is in concordance with earlier ideas such as Piaget's "Genetic Epistemology" and Maturna's "autopoises". Both of these attempt to transcend the philosophical problem of "causality", by moving towards the mathematics of "spontaneous coherence" as modelled by say "catastophe theory".
I am not saying that these are "solutions" to the inapplicability of traditional logic, only that they serve as useful vantage points in the development of the semantics of ontology. They are of course driven by the social forces towards ecology, but also more interestingly, perhaps. by problems of "the observer" in quantum physics.