Because of their apparently secondary role, alkaloids, mycotoxins, phenols, polyenes terpenes etc. found in plants are commonly referred to as secondary metabolites. Their presence has raised questions relating to the concepts of purpose and functions as these substances appear to have no explicit role in the economy of organism that produces them. This troubled biologists since long but soon it was realized that every property of living matter may not be purposeful. On the basis of the current evolutionary thought, mutations may well arise ( and indeed persists for many generation )which are neither expressingly beneficial nor harmful. Krebs designated such characteristics as ‘ballast’ and gave as an example alkaloids in plants, the presence of which generally baffles all attempts to account for them satisfactorily. This observation clearly shows that some materials in plants, having definite role and function, have produced other materials in the same domain without a defined role and function. Thus there is a control point in between, that baffles all attempts in true sense of the term. Knowledge of the control point that precisely controls secondary metabolites in plants may lead to precise control of these chemicals from outside employing remote control. Thus signalling control point in biological evolution is a challenge before the second generation nanotechnology – the molecular nanotechnology.