It has been known that new genes rapidly evolved in organisms (Long et al, 2003, Nature Reviews Genetics ; Kaessmann et al, 2009.Nature Reviews Genetics).How a newly arising gene is added to a previously existing gene network becomes a new and challenging problem.Meanwhile, the functions and phenotpic effects remain a key to understanding their evolution and their role to the evolution of organisms.By experimentally measuring the interaction of new genes with ancestral gene networks, we observed a rapid rate of origination of new links with many new hubs created recently, suggesting that the gene networks are changeable in evolution by new genes.What are the consequences of such changes in global gene networks on the phenotypic evolution? With the advent of gene silencing techniques and gene interaction analyses in model organisms, it recently becomes feasible to detect the functional and phenotypic effects of new genes in genomic scale.Using these silencing techniques and gene interaction detection in Drosophila, we observed several phenomena which revealed unexpected insights into a few important biological processes.We found that developmental genetic programs were species-specific and lineage-specific, rewired by participation of new genes throughout evolutionary processes (Chen et al, 2010, Science).We observed that the brains of humans and Drosophila had been changed by acquiring new genes recently in the critical portions of brains such as human neocortex and fly mushroom body (Zhang et al, 2011, PLoS Biology ; Chen et al, 2012, Cell Reports).We showed that single new genes can redefine the foraging behaviors in fruit flies (Chen et al, 2012, Cell Reports).We found that the new genes played critical roles in determining the sex dimorphisms (Zhang et al, 2010, Genome Research ; Zhang et al, 2010, PLoS Biology).All these phenotypic changes, contrary to conventional theories and beliefs, were found to be related to great changes in global gene networks, with emergence of some new concepts in understanding evolution and functioning of biological entities in a few levels from the genes to gene networks to organisms .