After learning more about how endosymbiosis occurred in the world today, I was inspired to revisit this thread. Here is a concept proposal which basically sums up a lot of thoughts people have had regarding endosymbiosis and combines them into a chronology.
Endosymbiosis
Background Information : Endosymbiosis is symbiosis where one cell lives inside the other. It is the root of atleast two eukaryotic organelles: the mitochondria, derived from alpha-protobacteria, and the chloroplast, derived from cyanobacteria. Most other organelles derived from variations of these original symbionts and the consequences of this union.
Endosymbionts are evolutionary viable because prokaryotes seek to streamline their genetic material as much as possible while maintaining essential metabolic services. It costs a lot of ATP to have an expanded genome, as more protein needs to be synthesized and transported, more ribosomes are needed, and more maintenance is required. Also, more genome means more reproduction time, and bacteria really depend on faster reproduction rates to compete with other bacteria. So as a whole, evolution was limited in the bacterial world.
There are few environments as safe for a cell as the cytoplasm of another larger cell, so some bacteria evolved the ability to live inside another bacteria. This meant they could ditch parts of their genetic code responsible for environmental tolerances, so these bacteria became incredibly simple (mitochondria and endosymbionts have some of the simplest genetic codes in the world).
Eventually, mutations built up which allowed the host cell to use ATP generated from the endosymbiont. This sounds crazy, but it makes sense. The endosymbiont had a vested interest in keeping the host alive; the host can survive without the endosymbiont, but the endosymbiont can’t survive without the host. As time passed on and as this symbiotic relationship continued, the endosymbiont basically discarded every component of itself except energy generation. This more intimate connection eventually led to a level of integration in which the endosymbiont depended on the host cell for reproduction, and thus, became an organelle: the mitochondria. The endosymbiont gained a safe hope, and the host cell gained an entire cell’s worth of energy generation without any of the maintenance costs.
Endosymbiosis represented an evolutionary leap. As previously mentioned, bacteria don’t like huge genomes because you need more ATP to maintain it and it takes a lot more time to reproduce. But because sooooo much more energy was now available, the reproduction and energy penalty for gaining a bigger genome was minimized.
It is actually a misconception that the nucleus came before the mitochondria. The nucleus was a result of genetic material exchanged between the endosymbiont and the host cell. It is likely that the “lipid genes” of the endosymbiont got transferred to the host cell, resulting in uncontrolled lipid production within the host cell. Lipids naturally form into hollow spheres in fluids (membranes), and some cells had their genome surrounded by this lipid membrane. This added a barrier between the cell’s DNA and genetic parasites and viruses, which helped protect an ever-expanding genome from being degraded. The protonucleus was formed.
This endosymbiotic freak was the ancestor of eukaryotes today. Virtually all eukaryotes have mitochondria and a nucleus, and most eukaryotes are rather similar in morphology. A certain eukaryotic population performed this process with cyanobacteria, and those eukaryotes were the common ancestors of plants. The notion that endosymbiosis happened a lot of times throughout history is probably wrong – all the features that followed suit from endosymbiosis, such as maintenance of genetic security, finetuning of endosymbiont, development of sexual reproduction, etc. arose under relatively delicate conditions caused by said endosymbiosis. In other words, endosymbiosis is a hard thing to pull off for the first few million years. Once a cell pulls it off and becomes properly eukaryotic, it would be extremely difficult for another cell to do the same thing while competing with established eukaryotes who dominate the niche said cell is seeking to expand into.
Applications to Thrive: I think there are three stages of endosymbiosis which can be observed here and in previous concepts.
- Obtaining an Endosymbiont
- Finetuning an Endosymbiont
From background history, there are several things to be considered. Of course, 100% realism isn’t necessarily 100% fun, so the script doesn’t have to be stuck to. Also note that much of this isn’t my concept, but is
General
- As Buckly advocates, endosymbiosis is pretty complex, so it should basically be a shortcut for more skilled players. If the player doesn’t want to do it, a traditional “upgrade” path should be offered which costs more MP and takes more time, but is much simpler.
- Progression is off in game, where you obtain the nucleus to get the mitochondria while in real-life it was the opposite way. To be more realistic, you should develop the mitochondria/endosymbiosis first to get the nucleus. Which one would be better for Thrive?
- I think the player should generally be the first or one of the first microbes to perform endosymbiosis on their world since it’s so intimately tied to being eukaryotic. At the same time, AI should have some capacity to initiate it so that plants can form if the player doesn’t want to create chloroplasts. Upgrade paths can help with this.
Obtaining an Endosymbiont
- Having cells evolved to enter other cells that gradually evolve to become endosymbionts is obviously maximally realistic, but not very feasible and would really depend on the AI. Depending on AI and having no autonomy obviously can lead to very unfun situations, so it should be avoided. Also questions around having one cell be inside another cell, which can be difficult to represent.
- Evolving the ability to even be able to carry out phagocytosis (atleast of entire cells) actually isn’t an incredibly ancient mechanism and is limited to a few archaea (I think) and eukaryotes. As such, there could be an “upgrade” path towards better phagocytosis.
- Metabolic/energy-based organelles should be the most important and prioritized endosymbiont products. I think this will emerge naturally; if you want to endosymbiont a toxin cell for example, you could do it, but that organelle costs a lot of energy to maintain when compared to basic prokaryotic parts. So they won’t be as viable until a mitochondria shows up.
- The benefits of endosymbiosis to the host are stripping a cell’s functions down to its base metabolic functions to minimize costs and maximize energy production: having all the benefits of energy generation in a cell with none of the costs. So I think for early implementations of endosymbiosis, endosymbiosis can be simulated by just creating an organelle based on the parts most common in a bacteria.
Finetuning an Endosymbiont
- An endosymbiont technically becomes an organelle when the host cell reproduces with that endosymbiont present. There is a period of time in between obtaining an endosymbiont and the emergence of an organelle where an endosymbiont is beneficial to the host but not a permanent part of it.
- Full integration of an endosymbiont allows it to become as efficient as possible, so transitioning to an organelle can unlock the full benefits of endosymbiosis.
Potential Roadmap of Integration for Endosymbiosis: As the developers commonly mention, many complex features yet to be incorporated will probably take multiple updates to completely be implemented, filled out, or optimally finetuned towards the best balance of fun and realism. There are a lot of ideas surrounding endosymbiosis, ranging from the simplest “consuming a specific microbe x times to unlock this organelle” to “full customization in organelles through endosymbiosis”. There is a lot of unknowns revolving the spectrum of these numerous interpretations of endosymbiosis. So I think it is important to establish a baseline endosymbiosis mechanism that is relatively safe, realistic enough, and fun enough that can easily be built up on, and then build up on that basic implementation with time.
Pre-Requisites for Suggested Baseline: Upgrade system present to offer an easy way out and to prevent players from embarking on and going through endosymbiosis much too quickly.
Baseline: A certain upgrade unlocks the ability to consume another cell for purposes other than straight up killing the other cell. Instead of the other cell getting damaged from engulfing based on the amount of time passed, after that time passes, the smaller cell turns into a eukaryotic organelle equivalent of its most frequent part, and gives a bonus to whatever process you are seeking to boost equivalent to the cell’s net production of said process. So if a cell minimized to just oxy-toxy produces the equivalent of 2 oxy-toxy proteins itself, you get that added onto your existing oxy-toxy production. If the cell is minimized to metabolosomes and produces a net ATP of 5, you get 5 ATP production added. If the cell is minimized to thylakoids and produces a net glucose of 5, you get +5 passive glucose production (my understanding of the mathematics of what is going on is probably wrong, but you get the general idea). So you are generally motivated to find either the simplest or most efficient microbes to maximize net production and minimize additional costs added on.
You keep that organelle equivalent for your cell’s entire lifespan. If you die, that microbe also dies, and you respawn without that organelle equivalent. If you reproduce, that microbe also reproduces, but you don’t have it in your next of kin yet. This allows to implicitly signal to auto-evo that a certain microbe is benefiting from being the endosymbiont.
You get one endosymbiosis “slot” as a prokaryote. You can choose from one of the last 5 (or whatever) microbes you’ve integrated into your cell to focus specialization/finetuning on, which is basically a new upgrade path available to the player. This upgrade path is applied to the function of endosymbiosis which basically reduces whatever “cost” the endosymbiont cell has in the process you are seeking to fully integrate into your host cell. A few upgrades can be offered which further minimize this cost until the final upgrade, in which you unlock the eukaryotic equivalent of the prokaryotic components.
This is a bit confusing, so let me explain with an example, and I think this is best explained with a metabolosome endosymbiont. Let’s go back to the 5 net ATP endosymbiont I mentioned before. Say that this cell actually produces 10 ATP through its existing metabolosomes, but maintenance results in the loss of 5 ATP, resulting in the net gain of 5. The first upgrade in this endosymbiont slot reduces the net cost within the endosymbiont cell by 25%, meaning you now gain + 6.25 ATP instead of +5 ATP the next time you integrate this cell. Another update increases this reduction by another 25%, meaning +7.5 ATP the next time. Another upgrade results in +8.75 ATP the next time. And the final upgrade represents the complete trimming down of the cell to its completely minimized form, unlocking the mitochondria. This represents the streamlining of the endosymbiont to become the hyper-specialized organelle seen in eukaryotes. Adopting and upgrading the nucleus can add more endosymbiosis slots, but I don’t think there should be an excessive amount. Maybe three at most?
I think the mitochondria being the first endosymbiont an average player achieves, just like in real-life, is implicitly incentivized since I think it serves the most benefits. You get the most versatile and ubiquitous benefit – more energy production to support more stuff/upgrades – so it’ll probably emerge as the best tactic since the entire game is about getting more energy. Players with a specific playstyle in mind are still able to do what they want, however; there’s a wealth of other metabolic strategies available, and you will still be able to upgrade until you reach the mitochondria anyways. I think endosymbiosis just serves as an easy way to simplify longer upgrade paths for parts you know you want. I assume there will be enough things to unlock that saving your MP will become important, so endosymbiosis helps you spend comparatively less MP to allow you to save it for other stuff you want.
I think this is easy to implement with the other metabolic pathway parts – just iteratively reduce the costs a thylakoid/rust endosymbiont would incur initially – but it’s a bit more interesting for things like toxin parts. Of course, you generally shouldn’t be eating toxin producing organisms (unless immunity concepts see that as good gameplay), but what would the benefit be in streamlining toxin cells? Reduced ATP costs?
Also as a general note, I might be incredibly wrong in my understanding of how the game calculates inputs and outputs with processes. But I think the general thing I am getting at can be understood.
There’s clear interest shown in the ability to have endosymbiosis be the ability to customize and create your own organelles by combining various parts, kind of like a mini-cell-editor for specific organelles. This would be really cool, but I wonder if it’s a Pandora’s Box in that it can release all sorts of balance issues, could make really bloated cells, could create an endless amount of organelles that will be difficult to keep track of in AI cells, etc. Such a system would need proper conceptualizing and stringent testing, which is why I think having a baseline endosymbiosis concept that can be added onto is a good idea.
Would the above baseline concept be a cool interpretation? Or am I neglecting something here? I am sure this idea has been thought of or brought up before, but this post still helps in that it organizes a lot of thoughts.