Computational modelling, explicit mathematical treatments, and scientific explanation

A computer simulation model, can produce some interesting and surprising results which one would not expect from initial analysis of the algorithm and data. We question however, whether the description of such a computer simulation modelling procedure (data + algorithm + results) can constitute an explanation as to why the algorithm produces such an effect. Specifically, in the field of theoretical biology, can such a procedure constitute real scientific explanation of biological phenomena? We compare computer simulation modelling to explicit mathematical treatment concluding that there are fundamental differences between the two. Since computer simulations can model systems that mathematical models can not, we look at ways of improving explanatory power of computer simulations through empirical style study and mechanistic decomposition.