Alternative processing raises many fundamental issues, perhaps none more important than the very concept of the gene itself. Prior to the discovery of alternative promoters, splicing, and poly (A) sites, a eukaryotic gene could be defined as a hereditary unit that codes for a specific polypeptide. However, this one gene-one polypeptide hypothesis does not work for alternatively processed transcription units that can code for two or more protein isoforms. We must therefore find some other way to define a gene. Although an exon has the minimal amount of information that is expressed as a discrete unit, we cannot define a gene as an exon because exons do not contain all of the information that we normally associate with genes. Perhaps the best definition that we can devise at this time is that a gene is a linear collection of exons that are incorporated into a specific mRNA. However, the term gene continues to be used in a more general sense when referring to a transcription unit or protein coding region. Alternative processing also presents challenges for genetic engineering. Some alternatively processed transcription units are known to produce isoforms that have antagonistic effects. Therefore, transforming a cell with an alternatively spliced gene may result in the production of a harmful rather than a beneficial protein.