How do you standardize factor of safety in design to have the most economical design, knowing that nature does not behave the same everywhere?

As a matter of fact, factor of safety depends on many various factors such as behaviour of materials, system of structure and environment. As you probably know, there are many different international codes for design of structures like AISC, ACI, ASCE, UBC...etc. In fact, each country has it's own rules for design of domestic structures and accepts only afew codes. However, it should be noticed that some factors are local and international codes can not cover them. For example the acceleration of earthquake depends on the local behaviour of soil and area and must be investigated separately by geotechnical engineers at site. Another example is the speed of wind which is an important factor for design of structures and must be determined by local investigations and codes not international ones.

Follow the load factors, material strength factors/ strength reduction factors provided in the latest edition of design codes (ASCE7-10, ACI318-11, AISC360-10, Eurocodes1 thru8, BS8110 & BS5950, etc.)