Variation among individuals affects human health, disease and medical or pharmological intervention. Additionally, this variation is the “stuff” of evolution. That is, evolution works by differential survival and reproduction among individual with variation in genetic traits. Thus, without individual variation, organisms cannot evolve. For the teleost fish Fundulus heteroclitus raised in a common environment a similar variation in mRNA expression exists; with a p-value of 0.01, 94% of metabolic genes have significant difference in gene expression among individuals within a populations. This level of variation is too large. Yet, the variation in Fundulus mRNA expression explains the large variation in cardiac metabolism (e.g., 11-fold for fatty acid metabolism), is related to genetic variation within a population, covaries with genetic and phylogenetic distance, and for at least one locus is dependent on promoter polymorphic sites. This raises an old paradox about genetic variation: if much of the variation is functionally and biologically important (affecting fitness) it cannot be maintained because of additive effects of selection against individuals with the many genes under selection. Our research tries to solve this conundrum.