Phagocytosis forms a vesicle around the organism or nutrients absorbed. Enzymes in what is known as a lysosome would then be engulfed by the vesicle, digesting it. However, if a cell with a faulty immune system were to absorb the energy radiating from the semi-permeable membrane, it would benefit and divide more quickly and efficiently than other bacteria, creating a more complex eukaryote. The Miller-Urey experiment is the best possible representation of abiogenesis, creating 25 amino acids from inorganic compounds, and the observation of protocells and the Endosymbiont Theory explains the evolution of basic life into more complex life.

That doesn't answer my question. How did the proto-photosynthetic bacteria become eaten by the heterotrophic bateria, but instead of being absorbed, it was told to divide when the cell divided, and effectlivly became a part of the whole organism? How was one chemically selective about the whole thing?

Endosymbiont Theory