The state-of-the-art of studies in molecular biology in the context of deve
lopment of the structural analysis of genomes and sequencing of total genom
es of various organisms, and the prospects of functional genomics in studyi
ng the fundamentals of life processes are discussed. The gene and genomic f
unctions result from complex interactions of genes and their products: deve
loping in time and space; the current methods of functional analysis are in
adequate to the intricacy of the living systems. As an approach to understa
nding complex functions, systematic comparative analysis of total genomes a
t the level of population and species is proposed, The results of comparati
ve analysis of the total genomes Of nematode, yeast, and bacteria are consi
dered, In conclusion, it is noted that, along with the broad use of compute
r technologies, development of the experimental methods for comparative ana
lysis of genomes and search for new experimental approaches to studying int
egral functions are needed. This is indispensable for the further developme
nt of molecular biology, to ensure its transition from elucidation of the s
tructure and regulation of genes and their expression products to a systemi
c analysis of the cell as an intricate ensemble of interactions.