Internal Parts & Metabolism

Gameplay
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Conceptualizing upgrades and variations for internal, metabolic parts has been a bit difficult because these processes ultimately represent biological processes which might require some work in implementing different environmental compounds. I’m reading through a lot of info on metabolism to get ideas, and while not all of them are bizarre and niche strategies, I’m having some difficulty getting decent ideas. External parts are pretty easy to think about since they represent traditional abilities in game design; metabolic parts, less so.

It’s not like we need a huge amount of additions, but we do need some anaerobic options for when we implement dynamic environmental compounds, which means examining phenomena such as the sulfur and iron cycles. So I wanted to create a thread which can focus on this issue to judge the appetite and capacity for implementing certain ideas.

To start, there are certain metabolic strategies which don’t require a massive reconfiguration of the way things work currently. Purple sulfur bacteria and iron reducing bacteria both are able to use the power of the sun to perform their processes, so we can include those as variants: improves the yield from compounds, but the processes become dependent on sunlight and make the cell much more sensitive to oxygen. With that, we would have four anaerobic strategies implemented in Thrive, two being dependent on photosynthesis. I’d like to include atleast 2 more anaerobic pathways, which is where the difficulty pops up. I would also think that these two additions should be anaerobic options in breaking down glucose if possible.

We can expand on the nitrogen, sulfur, or iron cycles since there are various important anaerobic phases that can result in interesting gameplay. Sulfate respiration involves the breakdown of organic matter with sulfate instead of oxygen, resulting in hydrogen sulfide. Nitrate reduction is a similar, albeit through a slightly more complicated process than sulfate respiration, resulting in the release of nitrogen. Of course, the issue is that we would have to include nitrate and sulfate in some capacity, though they would be atmospheric rather than clouds. And since nitrate and nitrogen and sulfate and sulfide loop into each other, that could result in interesting gameplay dynamics. Sulfate and nitrate are also limiting factors and influence biotic factors in ecosystems, so they could increase the dynamic and biological simulation nature of Thrive as a whole.

Before this thought train goes further, what are some initial reactions to this topic? Just to be clear, these mechanisms would be variants rather than their own individual parts.

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I agree that we will need some more anaerobic options for when we have low oxygen environments. You’ve already mentioned the sulfate path, so I’ll go ahead and list a couple other anaerobic organs.

Hydrogenosomes:
By far my favorite anaerobic part, these are specially adapted mitochondria that bypass the need for oxygen by using pyruvate (A product of glycolysis) as a catalyst. They get their name from their primary byproduct, hydrogen. These will allow for anaerobic eukaryotic organisms in Thrive.

Bioluminescence:
It is theorized that bioluminescence first arose as a defense mechanism against oxygen enriched environments by burning excess oxygen in the reaction and producing light as a byproduct. This part will not only give sensitive species a means of protecting themselves from oxygen, but will also allow us to finally have an excuse to throw bioluminescence into Thrive as a functional part (Yay!).

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It’s good that you conceptualized the “oxygen tolerance” qualities of bioluminescence. That plays perfectly into the fact that bioluminescence is much more common in prokaryotes as opposed to eukaryotes. Considering that most eukaryotes will naturally slide towards aerobic respiration for the higher energy yields, it is likely that bioluminescence would naturally become less viable.

The most annoying part about this anaerobic conundrum is that - in my opinion - there isn’t a very easy fix without somehow including new environmental factors. I guess the good news with sulfate and nitrate though is that they have immense relevance for life and the future stages as well, as they act as important limiting nutrients in many cases. Plants compete immensely for nitrate, relying on symbiotic relationships with nitrifying bacteria, and sulfate can influence growth rates and microecosystems as well. And as said above, implementing these metabolisms can result in interesting nutrient cycling simulations in Thrive; our ammonia-producing parts indirectly result in the creation of nitrate and v.v, while our chemosynthesizing proteins result in the creation of the sulfur needed to create sulfate.

It might be the case that a player can place down parts representing both “sides” of the nitrogen/sulfur cycle, but we can set up incentives so that players have to alter their body plan towards these different metabolisms, discouraging that. For example, one process could be anaerobic, while the other can be aerobic. Or we could have surface area effect each process differently.

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Nitrate and sulfate sound neat, but is adding more substances necessary? Can’t anaerobic processes be depicted without them? When you think about it, most processes in the game are already anaerobic in the sense that they require no oxygen. And the differentiation between anaerobic and aerobic processes doesn’t necessarily require anything more than a difference in output based on whether there’s oxygen or not. Let’s say you have anaerobic chemosynthesis (like we currently do) and then add aerobic chemosynthesis that’s more powerful in environments with oxygen but useless in ones without. Then you’d see aerobic chemosynthesizers prevail in oxygen rich patches and anaerobic chemosynthesizers in oxygen poor patches.

Here are some upgrades based on this simple approach:

Anaerobic Metabolosome – Produces less ATP but doesn’t require oxygen

Anoxygenic Thylakoid – Produces less glucose but doesn’t create dangerous oxygen

Aerobic Chemosynthesizing Proteins – Produces more glucose but requires oxygen

Aerobic Rusticyanin – Produces more ATP but requires oxygen

If you want to, you can also have eukaryotic versions of these. There could even be aerobic versions of other processes like toxin generation, although maybe that goes a bit far…

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I just worry that, since all our metabolic processes are based on environmental compounds, it might deviate a bit from the level of scientific detail we are trying to maintain. Actually, I guess glycolysis currently doesn’t base itself on anything, but that is its own category of metabolism.

I’m honestly not sure completely. What does everyone else think?

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I think we should avoid putting unscientific things in the game. But I also at the same time am in favour of not adding new compounds if we can get away with it. For example an existing compound that’s part of some other stuff in reality could stand in for that other thing in a process to avoid increasing the game complexity by adding a new compound.

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Would it be possible to treat a compound as both an atmospheric and cloud compound? Or atleast, easier than adding more compounds? 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.

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Well being a cloud and environmental compound are separate flags so in theory it should be possible to set both to true for the same compound. However, I’m pretty sure there’ll be a bunch of unexpected bugs or slight misbehaving of various systems that need to be fixed. So it is actually less error prone to make two “variants” of a compound like that. But that is also not without problems as the variants are really just completely different compounds and can’t stand in for the other in processes.

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Hey guys, member from the theory team here, I think there are very good ideas here, I just want to check if everything is somewhat cientifically correct. Also here

From what I know there aren’t neither acid lactic fermantation nor alcoholic fermantion in Thrive, which are both anearobic pathways - though I later should post something specifically about this topic.

I think you mean substrate (instead of catalyst), and I’m not familiar with this metabolic path, where did you find it?

This idea is actually very cool!

I am not sure I understand how this would be possible… Have you found this metabolic proceses somewhere or is it just a proposal?

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I got the information about how it works by quickly glancing over it’s wikipedia page so forgive me if I may have misunderstood some specifics. https://en.wikipedia.org/wiki/Hydrogenosome

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Wow! So interesting, I have never heard about this. I’m gonna do a quick research on it, but from what I’ve read it seems like it does not even provide nearly as many ATP as mitochondria does. However, I must point out that this is not correct

neither mitochondria nor hydrogenosome need glucose, they both use acetyl-CoA, a derivative of pyruvate, this process may happen already in the citoplasm (outside mitochondria) in the case of mitochondria (though it may also happen inside it), though it seems like in hydrogenosome it’s imperative to occur inside the organelle. The big difference between these organelles is the usage of acetyl-CoA, while in the mitochondria it is used with the final motivation of activating the electron transport chain, where ATP is generated, the hydrogenosome use acetyl-CoA directly to produce succinil-CoA, this is later transformed into succinate with production of 1 ATP, the final byproduct would be acetate.

In contrast with mitochondria, where the final byproduct must always be water and CO2, hydrogenosome produce acetate, molecular hydrogen and CO2, it means that, while mitochondria is capable of fully oxidizing pyruvate, hydrogenosome is not so it should never generate as much ATP as mitochondria does.

This metabolic pathway is actually pretty interesting though there are some missing crutial biochemical information that I will try to find out whether the scientific community has already discovered or not.

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From what I have been reading it seems like hydrogenosome is mainly used with symbiosis with methanogens or some other kind of prokaryotes capable of using molecular hydrogen in their metabolism, this would actually make a lot of sense, since the production of ATP, even though it is anaerbic, is as efficient as e.g. the lactic acid fermentation. Mitochondria produces 12 times as many ATP as hydrogenosome does, per acetyl-CoA.

If we could go into speculative biology for a bit, it would be theoretically possible to get hydrogenosome to produce 2.5 ATP per pyruvate, compared with the 15 ATP mitochondria produces, this will be just 6 times less instead of the previous 12 times less, making it advantageous over other anaerobic options, such as fermentation, yet without considering any symbiosis. This would be possible performing slight modifications to the real hydrogenosome.

If we did some big modifications to the real hydrogenosome it could maybe produce 3.5 or 5 ATP per pyruvate, making it, in the best of cases, only 3 times less efficient than the mitochondria. Though, this would be pretty much hard speculative biology.

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For anaerobic metabolosomes I don’t have anything specific in mind. I just remember them being an old idea. I’m guessing they would use some form of anaerobic respiration.

Anoxygenic photosynthesis exists in a number of different bacteria and uses something else like hydrogen sulfide or iron ions instead of water. It seems that some cyanobacteria can use thylakoids for anoxygenic photosynthesis [1, 2]. Although, thylakoids seem to be exclusive to cyanobacteria and chloroplasts, so other photosynthesizers presumably use some other structures.

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I actually thought you meant something completely different :sweat_smile:

Pretty nice, but yeap, anaerobic thylakoids are, in my opinion, kind of too much specific. But sure, we could use other photoautotrophs strategies, for example Halbacterium (or Haloarchea, specifically the Bacteriorhodopsin) which convert light energy into ATP directly, without firstly converting it into glucose, this of course has some pros and cons.

Ok, the only issue here is that ‘Metabolosomes’ is kind of an oddly specific amount of proteins that perform aerobic respiration, these would be completely different if other kind of respiration was performed. I mean it is simply a nomenclature problem. Of course the idea is thoroughly scientific. I’d say that nitrate reduction is the most common and the easiest to implement as ammonia is already into the game.

Sorry not to understand you earlier on haha :sweat_smile:, I hope the feedback was useful :smile:

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Let’s try to make this conversation more concrete so that we have a better understanding of just how to deal with internal part upgrades.

I think the question is how to introduce sulfate and nitrate in a way that makes it a bit more interesting than just adding another compound into the game, because we honestly would have enough parallels with other metabolic strategies to make things a little repetitive.

Let’s first focus on nitrate to make a more defined concept and figure out where there is gridlock.

Nitrate

Nitrate - specifically, denitrification - is an essential part of the Nitrogen Cycle. Nitrate is broken down by nitrate reductase to create atmospheric nitrogen, which is then converted into ammonia via either nitrogen fixation (converts atmospheric nitrogen to ammonia) or ammonification (converts organic nitrogen to ammonia). Ammonia is then converted into nitrite/nitrate via nitrification, and then the process starts again, with nitrate reductase breaking down nitrate into atmospheric nitrogen. It is important to note that there are non-biological processes which facilitate parts of the cycle as well; lightning can split nitrogen, allowing it to bond to oxygen to result in the formation of nitrate.

So at a very broad level, this is the ABC’s of the nitrogen cycle…

  1. Nitrogen gets turned into ammonia (nitrogen fixation or ammonification).
  2. Ammonia gets turned into nitrite/nitrate (nitrification).
  3. Nitrate/nitrite gets turned into nitrogen (denitrification).
  4. Repeat.

In Thrive

The fundamental idea is…

Adding Nitrate: A new atmospheric compound.
Adding Nitrogen Reductase/Denitrification: Breaks down glucose via utilizing nitrate as an electron acceptor. Rate scales with atmospheric nitrate. Results in nitrogen. Essentially metabolosome but utilizing nitrate instead of oxygen to burn glucose.

This will allow Thrive to have a solid anaerobic option for breaking down glucose while also adding more flesh to a very important ecological process. Fleshing out this system can result in an interesting dynamic where ammonia, nitrate, and nitrogen interact to create shifting “supplies” and “demands”. For example, an environment filled with nitrogen-fixating organisms would probably benefit from organisms who denitrify nitrate, as nitrogen-fixation depends on a supply of accessible atmospheric nitrogen. Not having denitrification could result in a reduction of the viability of nitrogenase and related parts as nitrogen reduces in supply.

Problem

The bad news is that the step before denitrification - nitrification, which results in the creation of nitrate - is largely a biological phenomena. This would mean that the nitrogen-cycle wouldn’t be a completely closed loop It would be quite a scientific gloss-over to have nitrogen-fixation directly feed into the supply of nitrates.

Nitrification itself essentially involves the breakdown of ammonia with oxygen to create energy. So implementing nitrifying bacteria would allow those cells to use ammonia as a food source instead of solely as growth compound. This sounds like it might be a lot for the game to handle and could result in a mess related to the growth mechanics, so I’m pretty iffy on this.

Potential Alternatives

Perhaps we can treat nitrate as a compound with a rather limited supply that gets introduced via environmental factors. While nitrification itself is largely a biological process, there are some abiotic processes which can result in the creation of nitrate/nitrite. For example, atmospheric chemical reactions or thunderstorms can create nitrate.

Maybe we can treat nitrate as a compound that gets introduced at random points due to environmental factors, which gets eaten up the more nitrate-respiring organisms are present? That would definitely be a unique mechanic which could make living as part of the nitrogen cycle a bit of a different gameplay experience.

It would also kind of make ammonia act as a limiting nutrient, which is a very important ecological concept which would be very cool to implement in Thrive. Since nitrogen-fixation reduces nitrogen supply, and since nitrate respiration increases nitrogen supply, there could be moments in Thrive where a saturated nitrogen-fixation niche within a compound reduces the amount of nitrogen available in the environment to reduce the total presence of free-floating ammonia. Less nitrogen available does mean less powerful ammonia production after all. Then, the environment would really benefit from a potential nitrate shock, where denitrifying bacteria reintroduce a good amount of nitrogen to the environment, thus driving ammonia supply back up.

The only issue is that, once again, nitrification is heavily dependent on biological processes, so it might be a bit too far from reality to make nitrate seem like a compound that relies heavily on non-biological processes.

Good News

Some good news I have for you guys is the fact that implementing a very simple representation of the sulfur cycle is possible in a relatively non-convoluted implementation…

Implement Atmospheric Sulfur - Would be present as a gaseous, atmospheric compound similar to nitrogen and oxygen.
Implement Sulfur Reduction - Uses sulfur instead of oxygen as an electron acceptor to oxidize glucose, resulting in the creation of hydrogen sulfide and energy. Essentially metabolosomes, but using sulfur instead of oxygen to burn glucose and releasing hydrogen sulfide instead of carbon dioxide as a by-product.

Since sulfide chemosynthesis results in the release of sulfur, and sulfur reduction results in the creation of hydrogen sulfide, we can have a very simple sulfur cycle. Attaching certain environmental effects to sulfur would reinforce the impact of the sulfur cycle on biogeochemical processes.

If nothing else, we can rely on the sulfur cycle as an answer to the pre-oxygenic glucose problem. If we want to, we can implement the nitrogen cycle in ways other than using it as a significant metabolic option, since that opens up various issues. Sulfur respiration is apparently a very ancient form of metabolism anyways.

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Apologies for the double post, but I have done some research on iron respiration and want to ask if something is possible before I forget.

There is an anaerobic chemical process which uses iron to breakdown glucose, releasing a reduced form of iron, carbon dioxide, and water as a byproduct (according to ChatGPT :smiley:). It is a very ancient form of metabolism and can be an additional form of anaerobic respiration to implement in Thrive.

Knowing this, would it be possible to have an upgrade which requires both iron and glucose to be gathered in order to produce ATP, or is this a bit of a hassle?

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Do we need a new compound type? The compounds in the game have been simplified at least once to reduce complexity to the player. Unless I misremember the environmental compound production just directly modified the ammonia amounts in the environment as for us ammonia kind of stands-in also for all kinds of ammonia derivatives in terms of processes.

It’d be much easier to implement as a separate organelle, but fundamentally an upgrade replacing the processes an organelle can do is not that much work to implement into the upgrades framework.

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I unfortunately am struggling to come up with a way to implement anaerobic processes with the current assortment of compounds/nutrients, and I’ve seen feedback from the community indicating that just using existing compounds broadly (like H2S and sulfur being represented as just “Sulfur”) to be wary of making certain compounds more abstract.

I understand wariness of bloating the game with a bunch of compounds, which has historically been a huge fear: if you add one, why not add 50 just to make it feel like the game has more substance to it? I think we are in a better position in the present to gauge whether or not to add a specific compound because we have a better conceptual understanding of Thrive now than ever before, so we can think of actual use cases rather than just throwing crap in.

We have a dire need to implement an anerobic process which breaks down glucose to fill that niche in a playthrough before oxygen arrives on a planet since metabolosomes/mitochondria are the only parts currently capable of that. Glucose would be almost useless pre-oxygen without such a part, as a big component of the Microbe Stage is having that early glucose boost. I’ve tried to find metabolic processes analogous to these parts with the existing compounds in game, but I haven’t had any luck with that so far. So I think it might be justified to add another compound, Sulfur, to fill that gap so we can implement sulfur reduction.

I think that since Sulfur would act as another environmental compound, it wouldn’t add too much complexity as long as we clearly explain what an environmental compound is. Players can readily ignore it if they don’t use it unlike a compound cloud, and there are other examples of environmental compounds present in game.

I was thinking of it being an upgrade to populate the upgrade menu for internal parts, since I really don’t have too much else for metabolic parts.

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I think it’s a bit late to complain about this. At least a bit. The game previously had amino acids, but those were removed and ammonia now fulfils that role. So we already are doing something as bad as considering hydrogen sulfide (as it contains sulphur) to be able to fill in for any role that requires sulphur. So at least sulphur kind of seems like a compound we could do without. I’d also like to note from a technical side that each cloud type compound that gets added requires more processing power. And each 4 new compounds require a new rendering pass for the compound clouds. Right now I think we have 2 empty slots before a new rendering pass is needed.

My suggestion for this situation would be to just remove hydrogen sulphide then and have it be replaced by sulphur if we truly need sulphur in the game.

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