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Most calcium carbonate deposits are made up of the skeletal remains of marine plants and animals that have fallen to sediment on the bottom of shallow seas after their death. If the conditions are right, these sediments can build up over geological time to form extremely thick layers.
Bones are made of calcium carbonate and a soft material called collagen. When the chicken bone was placed in the glass of vinegar, the acid in the vinegar dissolved the calcium carbonate so that only collagen was left. Calcium (the mineral in calcium carbonate) is needed to make our bones strong.