In this paper, we discuss connections of methods of modelling of fundamental phenomena which are important for foundations of theoretical biology with cognition process. In order to provide context for the last aspect, we discuss concept how mathematics could emerge from evolving dynamical systems imitating biological systems. One accentuates particular role of implication. Thus, implication has obtained now different status then alternative, conjunction and negation and is related to action of the main dynamical system. One accentuates also the fact that system of fundamental notions should be close to direct and most simple sensorial information. Methods of mathematical proof in relation to described reality is commented. Next, we specify important physical processes which should be modelled in order to provide foundations for efficient theoretical biology including mechanisms of biological evolution. Within above context, we discuss status of quantum mechanics, quantum electrodynamics, the Standard Model and vacuum medium mechanics with respect to possibility of creation of foundations for theoretical biology. In the conclusion, we state that the vacuum medium mechanics is constructed with particular intention to be fundamental theory for theoretical biology. One accentuates that electron theory constructedwithinthevacuummediummechanicsisofkey importance for further development.

physical aspects related to logic and foundations of mathematics, methodology for creation of theoretical biology and biophysics.