I think that’s a great idea. This way, you don’t really need an abstract punishment system or concept that “balances” against rushing to a different biome, it just completely depends on the cell itself. And the threat of going back to where your started adds weight to your decisions and adds to the story of life on your planet; do I risk adding these organelles which could be useful in the future but take up a lot of energy now, or do I just stay here and battle it out with the food chain and environment I know? This decision could tip the scale away from strategies which are perhaps a bit unrealistic as well, such as rushing to the surface and putting on a million thylakoids.
Reading through some of the forum discussion topics, I think the older enzyme concept and the feedback people had to that (Enzyme Concept) could prove to be a good consideration when dealing with topics such as Environmental Toxicity, Passive Enzymes, and Proteins coming up. It helps provide a concept similar to the “Protein Sliders bound by space” concept in the development forums, and I think it’s a neat way of organizing information and balancing systems.
I also agree with Sentiant when they rebuke the idea of random unlock proteins. I think it’s kind of a slippery slope as to exactly when said proteins will come into play, and with the way I see them through discussions on the development forums, I think they are too fundamental of a gameplay feature to leave up to chance. I think either letting the player unlock proteins or having them all unlocked in the beginning would be best.
About the worries of overburdening a new player with many different proteins if they were all available in the beginning, looking to the evolution of life on Earth provides a remedy. Early cells had much less to deal with in terms of environmental challenges, biological functions, etc. For example, they didn’t have to worry about oxygen poisoning for a while because oxygen would be introduced gradually into the atmosphere via biological/geological functions, and they didn’t have to deal with UV a lot because life (likely) started next to hydrothermal vents in the dark corners of our Earth. If we take this and apply it to Thrive - a simple environment with few things to worry about transforming into a biogeochemical system as entrenched and varied as the life that inhabits it - I think the player will naturally progress through the protein system as easily as possible, as they would only need to worry about a few proteins at first and will then begin to understand the wide variety as challenges come up. And then eventually, when the atmosphere is relatively stable as it is now, a player would know most aspects of the planet’s atmosphere, and would then have a base “level” of protein balances which they could tweak going forward.
And on another note, I also feel that this system represents biology. Life on Earth over the past few 100 millions of years grew so complex because of the relative stability of the environment, as body plans based on proteins and enzymes fine-tuned to the environment wouldn’t need to be constantly wiped out or completely reconfigured. Using this in Thrive, a more stable planet could expect to see more Earth-like or complex creatures, while a less stable atmosphere could lead to odd monstrosities and more simple life forms.