Inventors at Georgia Tech have discovered a broad and extensive new category of targets for interference RNAs (iRNAs) exclusive of mRNA. They have demonstrated that iRNAs may be used to manipulate biological processes that do not explicitly involve mRNA. New iRNAs can be directed at non-coding RNAs such as ribosomal RNAs (rRNA) and transfer RNAs (tRNA). An iRNA that targets a non-coding RNA is called a non-coding active in interfering RNA (nciRNA). Such nciRNAs cause degradation of non-coding RNAs in vivo and are highly active in biological assays. Because cells are sensitive to disturbances of the translational machinery, nciRNA-induced cleavage of targets other than mRNA, such as rRNA, offers an efficient mechanism to induce mortality in eukaryotic cells and organisms. The nciRNAs can be programmed with the desired degree of specificity, depending on the degree of sequence conservation, to selectively target and kill eukaryotic organisms at a selected phylogenetic level. Thus, nciRNAs can be directed at one species within a complex mixture of organism types.