5. Every Action Has A Consequence
As the Van Baalen brothers and the Doctor search the TARDIS trying to find Clara they happen upon the Architectural Reconfiguration System a network of circuits, a kind of genetic material, that can be used to create pretty much anything you want. Gregor Van Baalen thought it limited to machines, I dont think it is. I think those circuits are living parts of the TARDIS, almost like her eggs. When Gregor steals one of the circuits the TARDIS understandably reacts hostilely and defensively. Hes taken a part of herself. The network looks very similar to a Tree of Life a symbol found in many cultures, representing the interconnectedness of all things. In this philosophy, each piece of a world, a universe, a multiverse even, is dependent upon every other piece. The smallest disturbance will cause ripples across the fabric of space and time, affecting every other thing. Gregors actions have grave consequences for everyone on board, and lead to the death of his brother Bram. An act he feels no remorse for. When the Doctor describes the Architectural Reconfiguration System he refers to it as living metal bespoke engineering. This is an interesting choice of words and another allusion to River Song. The word bespoke means made to order. The Doctor refers to River as his bespoke psychopath in the series six episode Lets Kill Hitler. It is the TARDIS, however, who truly made River Song, not the Silence.