That's great. I like that. Something I've been doing is running it with initial conditions "each microbe gets a chloroplast, nucleus and cytoplasm and nothing else". I think that's an interesting way to start. See what you find.
Also I'm starting to think there is a relationship between the number of timesteps between auto-evos and the ocean mixing. So if the amount of mixing with the ocean is low then the protein which is coming out from the dying species can be instantly taken up by others and used to make more of them. So scavenging becomes really successful. I think this means you want a long time between auto-evos so that the effect on the patch as a whole can be really clear (like you getting rid of your chloroplast reduces the amount of sugar in the patch as a whole enough to make it not worth it for you, even if it increases the percentage of the patch's sugar you have).
Whereas if the mixing with the ocean is high then the number of steps needed is less because each species is more of an island. They have to make everything for themselves so the effect of giving up the chloroplast becomes evident quicker.
Like I just ran a sim where all the microbes gave up their chloroplasts, which makes sense if the patch has sugar but they just haven't detected that over time the amount will decay to 0 (though I guess if they can get their chloroplasts back at that point then that's cool).
I guess in general life in a sealed bottle would be weird, because they could just make some protein and then live off that forever, passing it round between them. They would just need a simple cycle to get some atp and that would be enough. So the dynamics will be weird.
Here's a run I did today with 1 mixing with the ocean and starting with 3 organelles per species, it's pretty interesting how it turned out.
F : 0 A : 4 P : 4 C : 4 Y : 6 L : 0 M : 3 T : 22 O : 0.0352048791827 .
F : 0 A : 3 P : 5 C : 3 Y : 5 L : 0 M : 2 T : 20 O : 0.035887939545 .
F : 0 A : 9 P : 0 C : 1 Y : 3 L : 0 M : 3 T : 17 O : 0.496922279518 .
F : 0 A : 4 P : 8 C : 2 Y : 3 L : 0 M : 2 T : 20 O : 0.23115696353 .
F : 2 A : 4 P : 6 C : 4 Y : 4 L : 0 M : 1 T : 23 O : 0.195507877075 .