I was doing more research, and I found that tortoises put an upwards force on the skeleton when it's growing new keratin on its shell. What if when the tortoise has MBD, or the bones aren't very strong from lack of humidity or too much protein, the bones try to grow with the the upwards force and cause the lumps we call pyramiding. It would explain why after the first few years of life you can't really fix it. What does everyone think?