Employed by Dr. Henry Wu, the version number scheme was designed to modify and “improve” the genetics of InGen’s dinosaur specimens if any glitches were found, similar to computer software updates. If deemed necessary, the entire then-current dinosaur populations on Isla Nublar would eventually be replaced by newer release versions. As evidenced by the park’s dinosaur population tally, the most up-to-date version numbers by the time of the Isla Nublar Incident ranged from 3.0 to 4.3.
Dr. Wu was planning to create a version 4.4 for Phase Two of the park’s development, replacing all of the current stock of dinosaurs in the process. Believing that the current population was not adequately consistent with the public’s (often inaccurate) perception of dinosaurs, Wu intended to create slower, more manageable dinosaurs, which would be both easier for the park’s staff to care for and more in keeping with future guests’ expectations. However, John Hammond was strongly opposed to the idea, due to his belief that the dinosaurs would no longer be “real” if they were genetically “domesticated” for public viewing.
Sources: Jurassic Park, by Michael Crichton, pages 122-4, 129-30 (Fifth Reprint)