Just noting that RuBisCo is probably the most well known protein involved in carbon fixation, and is easily pronounceable.
I also discussed this gameplay element with Untrustedlife before:
Mentioning also here that RuBisCO was almost going to make it as a separate organelle in the game, but turns out it is already in the game, just as an implicit part of other things.
My reply about this in the specific RuBisCO thread.
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it could be made so that the parts with RuBisCO (other than the membrane bound ones) don’t have RuBisCO in them and it has to be added and it would make photosynthesis more realistic(with a lot of RuBisCO and thylakoids in chloroplasts and prokaryotic algae) and cyanobacteria would be actually cyanobacteria and not just a thylakoid in a membrane.
there would need to be an announcement or something before it happened though to make sure players don’t get angry about going extinct because they had no energy storage compound available due to being prokaryotic and the size of a eukaryote
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(I’m not a theorist, so take this with a grain of salt. I did my best to google stuff.)
Before you go with gluconeogenesis for the new organelle, I think it’s important to ask where the carbon comes from. Gluconeogenesis uses certain organic compounds as its source of carbon. Where do the compounds get their carbon from? Since the new organelle is supposed to be a source of glucose for cells that get their energy from carbonless sources like temperature differences or iron, the energy source doesn’t supply them with any carbon. If they want to get carbon, they need to either become heterotrophs and hunt organic compounds (which would kind of defeat the point) or produce their own compounds from inorganic sources, most likely by fixing carbon from CO2.
Carbon fixation is already in the game even though it’s not named explicitly. It’s how other autotrophs get their carbon when they perform photosynthesis or hydrogen sulfide chemosynthesis. That’s why those processes scale with the amount environmental CO2.
I think that having to work for the carbon in your glucose would be more realistic and more consistent with photosynthesis and chemosynthesis. So if you want to get glucose as an autotroph, in my opinion you should have to fix carbon for it. And the new organelle would be the way to do so. Here are some name suggestions:
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Carbon Fixing Proteins , proposed by Buckly. It was rejected, but I think it could be considered again since there are fewer options without gluconeogenesis. You could also use similar terms like carbon assimilation, carbon dioxide reduction, carbon fixing enzymes, etc.
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Find some new fitting enzyme, e.g. Alpha-ketoglutarate Synthase (also called 2-oxoglutarate synthase or KGOR). I think it’s linked to CO2 reduction in the reverse Krebs cycle, so it’s basically analogous to RuBisCo. It’s not exactly catchy though, and it’s also not nearly as commonly used for carbon fixation as RuBisCo.
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Ignore that it’s used in photosynthesis and call it RuBisCo anyway. It at least sounds good. RuBisCo is also used by some chemoautotrophs [source]. The same problem kind of exists for generic carbon fixing proteins as well, anyway.
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Make up a new name. Maybe Glucose Synthase (which isn’t a thing AFAIK but sounds like something that makes glucose) or Glucose Synthesizing Proteins.
However, a question arises: Why would carbon fixation come bundled in with photosynthesizing and chemosynthesizing organelles but be a separate organelle with Rusticyanin or Thermosynthase? That might be confusing. Here are some options that might avoid the confusion:
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Explain this in the organelle descriptions. “Thylakoids get carbon for the produced glucose from carbon fixation”, or something like that (although technically thylakoids on their own don’t fix carbon).
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Remove carbon fixation from Thylakoids and Chemosynthesizing Proteins and have them produce ATP instead. You can keep the eukaryotic equivalents the same if you want because they would probably fix carbon inside themselves since they’re plastids. This would be a bold change. It would make the organelles consistent, but it might also make the game harder for new players. On the other hand, it would open up new potential strategies, e.g. can you live as a photosynthesizing mixotroph without carbon fixation?
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Go back to the upgrade idea instead. Add a “Carbon Fixing” upgrade to Rusticyanin and Thermosynthase. Yes, it does require that upgrade for any possible new organelles, but are there that many of those planned? It’s pretty simple, you don’t have worry about naming as much and you don’t have to deal with how to control the ATP to glucose conversion. Personally I think I’m actually a fan of this one.
What do you guys think? Do you agree that carbon fixation is the way to go? Should the new organelle still be an organelle? If so, how do you deal with photosynthesis and chemosynthesis? Do any of my name suggestions help?
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I just casually added to the issue on Github a note about thinking about where the carbon comes from, either from CO2 or handwaving it away by saying it gets recycled from when the glucose is used to produce energy again (respiration).
Ah, that does make sense. I was aware that it’s also used in most photosynthesising organisms (that’s why it’s so abundant in real life) but I figured it could also apply to most imaginable energy sources.
The actual carbon fixation IRL takes place outside the thylakoids, though in for example plants it takes place outside the thylakoids but still inside the chloroplast. One option could be to separate the carbon fixation from thylakoids altogether, and only have it as a separate organelle (and funnily enough, light-dependent organisms that can’t make their own glucose do exist). In that case, you would probably want to still have chloroplasts (and equivalents) directly produce glucose.
You should read the exact plan as outlined in the issue:
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Gluconeogenesis does indeed recycle carbon from inside the cell. However, that still doesn’t really answer how the carbon originally enters the cell. Sure, that could be the handwaved part. Maybe there’s invisible carbon fixation or an unknown source. I still personally feel that it would be weird if photosynthesizers need CO2 to turn an energy source into glucose but cells with the new organelle don’t. But maybe that’s not a big deal.
About these other ideas like separating carbon fixation from Thylakoids or going back to the upgrade idea… Yeah, they do divert from the current plan. They could still be worth considering in my opinion, but sorry if they are diverting too much from the discussion. We can stick to the current plan if that’s preferable.
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I mean we’ve gamified so much that there’s a free glucose cloud that appears out of thin air next to the player when they return from the microbe editor. Compared to that this is a really minor nitpick.
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Abstract according to valence:
The microbial nitrogen-cycling network | Nature Reviews Microbiology
Considering that elemental sulfur is a solid, it should be like current iron.
Sulfates, nitrates, hydrogen sulfide and ammonium serve as environmental compounds.
Sulfates and nitrates should be like current O2 and CO2.
Hydrogen sulfide and ammonium need to be absorbed by cells based on environmental concentration and absorption capacity, and enter storage to work. (Create a process of absorbing (synthesizing) material based on environmental concentration based on the size of cell surface area and membrane type?)
Hydrogen sulfide still has naturally generated clouds in Hydrothermal vent and other special patches.
If ammonia entering the breeding progress bar is regarded as amino acid synthesis, should it be regarded as a controllable process? By coordinating with the process regulation function, cells can reduce consumption by slowing down growth, and photosynthetic bacteria can hibernate at night. This process may also be combined with the environmental tolerance of cells, reducing the rate and efficiency of amino acid synthesis in less adaptable environments.
And the carbon cycle(Not considering methane):
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“I wonder if we can rename hydrogen sulfide to just “Sulfur” and have it treated as both a compound cloud in the form of hydrogen sulfide and as an environmental compound as atmospheric sulfur/sulfates.”
As a high school chemistry teacher: please no.
Hydrogen sulfide en sulfates are completely opposite in redox value. Put simply: while they all contain the element Sulfur, they are complete opposites in terms of chemical reactions.
That applies to their role in micro-organisms as well. It would be the equivalent of unifying your “glucose” and “CO2” compounds to a single compound and naming it “Carbon”.
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This is equivalent to abstracting multiple compounds into a single chemical element. This will turn Thrive into a chemical element collection game, which is too bad. The conversion of chemical elements with different valence in different compounds is an important form of material cycle.
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Consider hydrogenosome and acetate’s gluconeogenesis
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hhyrylainen changed his pfp in the development forums?!
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Yeah, on Discord too. The new Discord username update thing changed his profile picture so he just decided to go ahead and ensure that the eye truly sees everything now.
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Do we know how much the performance has improved in Godot 4 physics engine?
I know that they changed from bullet to there own homebrew version.
I don’t know. If such a benchmark exists, it should hopefully be relatively easy to find with google.
Which has never lead to an increase in bugs… Just kidding, that’s definitely a way to have a fresh batch of new bugs by reimplementing something. Still for us this will be irrelevant if the switch to using an external physics engine goes well. Also funnily enough for Godot 4 there is already a premade integration module to swap out the Godot physics for the Jolt physics engine.
Attempted to design an extremely long rod-shaped cell. Due to the fact that the current engulf ability mainly depends on the size of cells, we will obtain the following situation:
Even if the engulfed cells are reduced, they still exceed the range of predators.
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Thank you for the screenshot. It’s pretty reflective of a point in the OP!
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Current engulfment , membrane generation and Hitbox:
Based solely on size, it’s still too rough. More consideration should be given to cell shape.
According to the data I have consulted, iron respiration (not the Chemosynthesis with oxygen to iron oxide in the game now. Why does the nature have pure iron, and shouldn’t the reducing agent be Fe2+ ?) is an extracellar respiration, because Fe3+mainly exists in the form of solid precipitation, which means that it is unrealistic for cells to collect and store Fe3+.
Fe3+ can be used as an environmental compound and its concentration can affect the rate of iron respiration. But this homogenizes with oxygen, and the gameplay is too monotonous. (NO3- can do this directly because it participates in the Nitrogen cycle as a play method)
Considering that Fe3+has a certain solubility and mainly exists in the form of solid precipitation, its concentration can be unevenly distributed within the region. In the current game, there are iron blocks (the red ones should look like Fe (OH) 3 precipitates). If there are Fe (OH) 3 precipitates, a decreasing Fe3+concentration will be distributed around them. This concentration can be opened by the chemical receptor to the Fe3+concentration field, unlocking the tendency of AI towards Fe3+behavior.
I would like to know if there is a corresponding embodiment of this surface adjacency bonds in reality. I like this design, perhaps it will encourage cells to wrinkle.
Based on the knowledge I have, if Surface-adjacency bonuses come from adjacent cell membranes, those biochemical reactions that rely on membrane structure should benefit, especially utilizing ATP synthesis for oxidative physiology. Also, will external structures such as flagella affect the Surface-adjacency bonuses of internal structures? They do not affect the internal structure and cell membrane proximity.
A simple and intuitive method for calculating surface area is good and easy to understand. However, when calculating surface area and exposure, it is required that this is also the exposure of the entire cell. Otherwise, players may design a spring, cavity or fishbone. Perhaps it is necessary to use membrane generation for tuning?
One problem is that if the part placement mechanical is added, the existing Organelle replication mechanism will have a greater impact on cell design. The newly copied Organelle will appear outside the cell and destroy the original Surface-adjacency bonuses.