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Yes, but not in the organs that large forms of life have, such as stomach, intestines livers, etc. Instead, they have what are called vacuoles. These vacuoles are small, circular pockets inside the amoeba spontaneously creates that can either digest food or excrete waste. When an amoeba eats, it engulfs its food with its pseudopods, or blob shaped projections. The food it engulfed creates a little pocket, or vacuole, that is then used to digest with and later, the vacuole is released from the amoeba containing the waste it created from digestion.

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