  Thermodynamic tools are well suited to connecting evolution of protein
functionalities to mutations of amino acid sequences, especially for neuronal
network structures. These tools enable one to quantify changes in modular
structure and correlate them with corresponding changes in observable
properties. Here we quantify modular rodent-primate changes in amyloid
precursor protein A4 and \b{eta} amyloid fragments. These are related to
changes in cortical connectivity and to the presence (absence) of plaque
formation in primates (rodents). Two thermodynamic scales are used, descriptive
of water/air protein unfolding (old), or fractal conformational restructuring
(new). These describe complementary aspects of protein activity, at
respectively higher and lower effective temperatures.
