Ok I think I will have to focus down on one biological process.
Symbiosis might be good because its quite vague and you might be able to apply it to lots of things.
It could also be used quite easily to espouse a kind of socialist agenda. I'm not really sure if this is good or bad.
Something more specific like Protein Synthesis or Neurotransmission might be easier, because it's a specific process. It's also not so easily manipulated into a political metaphor, which might give more freedom.
I think there will need to be meta-commentary- in the form of a presenter- maybe with cloying-madteacher face paint (live action filmed).
Then we close into the cell, the nucleus, there is a voice over describing the process and the different players of the biological process have different characters.
The philosophical implications of the process is explored, either by the presenter or by another method. Preferably by another method, because we don't really like the presenter, she represents a kind of manipulated view of the scientific process.
References to pop culture and everyday mundane things are used.