You definitely answered the question of whether maths is still needed for MSMs! bond graphs! thank you.

How do bond graphs scale, even single enzymes/transporters appear complex, a whole pathway would incredibly complex in terms of a bond graph? The second issue is abstraction, we always abstract to more course grained models in order to deal with the complexity. Can one do abstractions with bond graphs?  

The need to explicitly represent conservation laws distracts from the scale of interactions, namely the dynamic behavior and responsiveness of cellular populations (which are explicitly not steady state), from which the richness of biological behavior arises, is the source of generation of biological phenotype and manifestation of disease, and is the functional/operational level of pharmacological control. The future of integrated multi-tissue/organ whole body modeling is still in a discovery stage where there must be opportunities for different researchers/groups of researchers to explore different means of binding and integrating across scales based that may (almost certainly) vary depending on intended use.