Radio Lab has an interesting segment where a scientist explained how, in the primordial soup, certain large molecules had a symbiotic energy exchange with smaller outside molecules, then at some point the larger molecules started absorbing the smaller molecules into themselves (they are not sure why, possibly just an accidental mutation that turned out to be beneficial and was passed on during replication...or possibly the Hand of God, if that's your dish), which then began to replicate INSIDE the host, thereby laying the groundwork for complex cellular development.

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I'm sure I have some of the exact terminology a little wrong, but that's the basic idea anyway. If anyone could identify that edition of Radio Lab, I'm sure it's freely available, and would be a good listen.