Regulatory conflicts between host and symbionts (i.e. signaling molecules of host and symbiont interfering with each other) promote host--symbiont integration, providing a narrative for how a transition in individuality may take place in a tight endosymbiotic relationship.

Although we enforce the endosymbiosis, host and symbiont normally adapt in such a way that preserves their regulatory autonomy. Only when we include regulatory conflicts, do host and symbionts evolve to communicate and to establish control mechanisms between them.