The paper presents an illustration of the thesis that economic science cannot exist without the political/ideological background, with reference to liberally focused direction of economic thought an example of the development of the Russian national innovative system in a context of the European research space. The author asserts that conflicts of interests between the households, state and enterprises are often caused by distinctions in the paradigms of technological civilization, tradition, shaping ecotechnological civilization and arising biological civilization. The solution can be found by developing the bases for ecotechnological civilization, first of all methodological foundations, using methodological individualism, accompanied by alternative concepts.