Passive Enzyme/Protein Slots System

Ah that’s an interesting idea. Upon thinking on it, I do have some reservations though. It feels to me similar to the “Genome Size” system, but instead of storing the proteins in your genome you store them in your membrane. It would be more accurate for proteins to be genetically limited and not membrane limited. Also, AFAIK proteins don’t reduce membrane transport functions. I think the benefit of the Genome Size system is that it allows us to give functionality to the nucleus and other similar DNA storing organelles.

This is a cool concept! Maybe the player could “paint” different parts of their membrane to give different concentrations of proteins - even if it doesn’t change the gameplay much, it’d still be a nice way to give the player some way to customize their prokaryote.

This does make me wonder though… will bacteria have any internal structures at all? If these are stuck to the membrane, it wouldn’t make sense to call Thylakoids “Thylakoids” anymore, but then how would structures like the ones in chloroplasts arise? What about the funky structures on the inside of a mitochondrion? Were both organelles’ ancestors relatively “hollow,” but their anatomy was highly specialized once they became assimilated and thus it’s not something you’d see swimming around? Or would structures like that (similar to the way proteins are represented in Thrive now, I suppose) still be present?

Also, in response to Nick’s message, perhaps one really specialized protein could have a large amount of gene space dedicated to it, but if you want to fine-tune its effect on your cell, you could lower its concentration on your membrane. That way both systems can work at the same time without one being redundant.

It’s supposed to work with the Genome system, this system would be used for distributing energy producing proteins on the cell while other proteins and enzymes, like catalase or anti freeze agents, would be stored inside it. Now that i think of it, the concentrations of these proteins in the cytoplasm could also be altered with this system making a cell more resistant to a specific hazard.

I thought about that, in the concept i added a few structures under the proteins, one of them being the nucleoid and another a carboxysome. Also from what i’ve seen, thylakoids are inside the cell, enveloping its nucleoid instead of being on the membrane.


As for mitochondria structures, that’s the double membrane they had when they were free living cells, but it became wrinkled to have more surface area and be more efficient. That adaptation could also be used by free living cells in the game.

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Ohh I see. It’s an intriguing idea. Would the proteins be visually represented in the membrane?

I am still leaning against it though. I would prefer not to introduce another system on top of the Genome Size, I think it can begin to add a lot of detail to this aspect of the game. I think it’s better to have the energy producing proteins stay as they are, or convert them into the genome size system with the rest of the proteins. Plus I’m reluctant since most of these proteins are not actually found in the membrane.

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Yes, they would be distributed in symmetrical patterns as i showed in the concept. I guess the current models could be used for that or we may make new textures.
Which proteins aren’t found in membranes? I think at least rusticyanin and aerobic proteins are, don’t they?

The results from the player feedback polls are in and there were some interesting results:

Only 11% of people wanted to keep prokaryotic parts as placeable hexes. Other than the people who chose “Other”, the remainder were narrowly split between the Genome Space system and the Membrane Proteins system. In the interests of reaching a conclusion on the subject, here are the thoughts I have on choosing from between the two systems.

Genome Space System
As I mentioned before, I think it gives cool functionality to the nucleus and other DNA storage structures. It also makes it easy to balance proteins by changing how much gene space they take. A nice side effect is that we don’t have to create 3D models of every protein under the sun (and find ways to make all of them look distinct), because will not be visually represented as hexes in the game. Which means we can implement a whole bunch of them soon. Cells will also look more realistic because proteins are invisible at this scale, so you’ll only see the membrane type, nucleus, and organelles.

Membrane Proteins System

It’s a cool idea, but I see several problems with it:

  • Many of these proteins do not exist in the membrane (sorry DonGoro forgot to reply to your post earlier, so the next sentence is my reply). For example, thylakoids, nitrogenase, lysosomes, and antifreeze proteins.
  • How would you represent this visually in the game? Would there be protein models floating slightly above each cell to represent being embedded in the membrane? I don’t think we have the ability at the moment to actually make them visually embedded in the membrane. Plus, proteins would not be remotely visible on the membrane at this scale.
  • It kind of overlaps with Organelle Upgrades. Organelle upgrades already allow for organelles and proteins to be improved beyond their base efficiency, and then this would further allow efficiency to scale up or down, so organelles would have to be balanced for two different dimensions of possible efficiencies.

Some Extra Points
The question to consider is what to do about the proteins currently in the game as placeable hexes. I think for the sake of both realism and internal consistency, these should be removed as placeable hexes and added to the Protein Slots sytem.

Summary

So to conclude please leave your feedback and which system you prefer. The sooner we settle on a system, the sooner we can start implementing more of these Proteins into the game. @Buckly also let us know what you think of the alternatives.

It’s a really tough decision. A good thing to keep in mind is while 80% of the people voting wanted either no placable proteins or Narotiza’s method of placing proteins, that’s only 80% of 37 people who voted on this. So I do admit I am hesitant to act on such a statistic, as well as concerned that I may not have properly communicated just what the options meant. But in an effort to move forward with this discussion we can at the very least assume it’s possible that the wider fanbase would roughly have the same views.

Personally, while I like Narotiza’s proposed method of handling visual placement of proteins I feel that having a secondary system on top of another new system would be a bit more than we need. More options are always good but we dont want our menus to become too cluttered with separate features and menus as they would become rather difficult to navigate, especially for new players.
I’m still a little hesitant on the idea of removing the protein parts as that will leave prokaryotes with very little variety in the way of placable parts. But who knows, maybe this will make progression feel more rewarding as you are granted more possibilities and customization when becoming more complex?

That being said, when it comes down to it I am leaning torwards completely moving the protein parts to be handled by the storage system as opposed to having two seperate new systems for handling the proteins.

Though I am curious if it’s plausible if we could keep the protein parts as a sort of concentrated spot of proteins rather than a representation of amount in the cell that you could place after equipping your cell with the protein. I’m not sure if that would be realistic.

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If you check the Appendices, we’ve still got a decent number of placeable organelles to complement the Proteins. These include:

Microbial Jet
Sensory Cilia
Contractile Vacuole
Secretory Vacuole
Bioluminescent Dot
Ferroplast

However, I did just think of one downside of making all Proteins placed in gene slots. How do you treat the compound processing proteins in the new protein slot system? In the current system, if you want more nitrogen production you place more nitrogenases. How do you do that with protein slots?

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In the original post I stated you could increase the effectiveness of your proteins and such by adjusting the amount of space they take up as a sort of parallel to organelle upgrades. The larger amount of space your protein takes up, the more effective it would be.

Edit: Nice to know we already have some parts planned out though, I should really take the time to look at the GDD more often as I have only sparingly glanced at it in the past.

Hmm, that feels a little clunky but I can’t put my finger on why, and I don’t know how well it meshes with the current Organelle Upgrades system.

This makes me wonder now whether it’s best to just stick with placeable proteins for now, since it’s the system that seems to create the least problems (or perhaps reconsider the membrane proteins system). I’ll think on this for now to see if I can come up with anything to help.

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Oh! I just had an idea.

Proteins have a little descriptor that labels them as Nucleic Proteins or Cytoplasmic Proteins:

  • Nucleic Proteins do not scale, they either exist in your cell or they do not. The moment they are enabled, they perform their full function. This is like antifreeze proteins or lysosomes, you either have them or you don’t. You can still use Organelle Upgrades to improve their efficiency, but that’s it.
  • Cytoplasmic Proteins add an effect to the Cytoplasm hex. This means that it scales with the number of cytoplasm hexes in your cell. Cytoplasmic proteins are the ones that enable processes, like rusticyanin or metabolosomes. When you enable more cytoplasmic proteins, this adds processes to your cytoplasm hex. This will be easy for the player to track, because let’s say the player evolves metabolosomes. Now every time he places a Cytoplasm hex it shows how much extra “Aerobic Respiration” it adds to his cell. If you think about it, this is similar to what we’re already doing with the Prokaryotic Structures, since those hexes perform a special function PLUS the base Glycolysis.
  • If we really want to flesh it out, we can add a third descriptor called Membrane Proteins. These scale with the length of your membrane (the number of exposed hex edges). This applies to receptor proteins and perhaps a few others.

At the start of the game, the only gene you have unlocked is Glycolysis Proteins. This is why the default Cytoplasm hex performs Glycolysis.

A benefit of this system is that it allows for three different specializations based on the types of proteins you use the most:

  • Cells that mostly use Nucleic Proteins will want to stay small, since their proteins can no benefit from the cell being larger.
  • Cells that use Cytoplasmic Proteins will want to grow large, since each additional Cytoplasm hex adds more processing power. However, they will still be limited by the natural penalties of growing too large, so ideally they won’t snowball into massive cells.
  • Cells that use Membrane Proteins (if we decide to add that descriptor too) prefer to have lots of surface area, since this maximizes the use they get out of their Membrane Proteins.

Thoughts?

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Just changing the protein’s concentration in the cell feels like changing a pie chart, when the gene space itself is already a kind of pie chart, so that’s why it might feel kinda redundant and clunky even if the two systems are different.

I like your idea! (which you posted while I was writing this, forcing me to rewrite the whole thing :angry:)
I was gonna suggest something about being able to place every protein as a hex to maintain control over concentration and visual variety, but adding different classes of proteins is pretty interesting. (Though Nucleic proteins would all have to be in the nucleus in order for them to make sense)

I also like the way you think of cytoplasmic proteins as a modification to cytoplasm, because it’s bugged me so much to see proteins either somehow removing glycolysis entirely, or having a reduced “protein glycolysis” that makes it seem like the protein itself is performing those processes, which is really misleading (though I know there isn’t really a better way to communicate that with the current tooltips, the description for Chemosynthesizing Proteins does say that it “also turns Glucose into ATP,” which is just innacurate - it’s done by the cytoplasm!!)
I would be ok with the glycolysis being just as efficient when with a protein though, I guess it depends on how much space proteins take up, displacing the cytoplasm. If they’re super small, it would make sense, though even super small proteins could be super clustered.

I also have a bit of a question: I assume each hex can only have one cytoplasmic protein? How would a hex be able to have a cytoplasmic protein and still be able to perform glycolysis? (Which you say comes from glycolysis proteins? …Unless they’re nucleic proteins, in which case, would it really make sense to call them nucleic proteins?

Also: Is there any reason a cell with a bunch of cytoplasmic proteins couldn’t just have a bunch of different proteins of different concentrations in the space of one hex? I mean, realistically it should be possible, would it hurt much if we just looked over it though?

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Wonderfully thought out idea, I really like this concept! From what I understood of what you were saying it will basically enable the player to upgrade the functions of their basic cytoplasm hex by customizing what it does via the protein storage system. Really clever idea.
I’m afraid I dont really have anything to add to this at the moment, but I am okay with going with this and support the idea.

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Oh, I understood it as you could place down cytoplasmic proteins like we can currently, rereading it though I’m pretty sure you’re correct, duh.

So in that case, a one-hex cell would be able to use any amount of proteins, so long as the player has them unlocked, and growing large wouldn’t be an absolute necessity if you wanted to use more than one protein?

Would it be too unrealistic for a cell to be running multiple processes, all at full efficiency, in every single hex of cytoplasm it has?

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After reading through everything once again, and thinking about our discussion and all the points everyone has made, I believe I’m actually starting to lean towards keeping our prokaryotic parts while introducing the protein system for passive effects for now. My reasoning is that Thrive as it is was built around the placement of parts to build your cell up to ever increasing complexity, and completely removing the prokaryotic organelles creates a bit of a void in that area as we dont really have much to fill it with at the moment. It’s alot of work for an uncertain reward.
That doesnt mean I am entirely against the idea of converting our prokaryotic protein parts into this system, But I would prefer to go about it slowly rather than dunking ourselves headfirst into a completely new system.

That being said. Here is my decision; If we all like the idea of the protein slots system I say we go ahead and implement it. It would be a nice big feature to release alongside our environmental hazards such as cold once we are ready for that. All the while we keep our current prokaryotic parts alongside the system.
This way we can get a feel for the new system and see how we like it as a place for passive bonuses, and then decide on where to go from there.

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Apologies for not replying earlier, classes went from 0 to 100.

Exactly. It’s actually quite realistic, since there are many proteins that are dispersed throughout the cell’s cytoplasm that perform many of its vital functions, and these proteins are tiny and evenly distributed across the cytoplasm. In gameplay terms, the limit on this would of course be gene space, and also that if you wanted to become a eukaryote to use eukaryotic organelles you’d have to get larger.

@Buckly Sounds great! It would be good to at least get the Protein Slots system into the game first to see how it feels like, before we take a more drastic step like removing all Prokaryotic Structures to implement those into Protein Slots as well.

Plus, if we are to think in terms of priorities, I think first we should focus on implementing Organelle Upgrades, then Protein Slots and Environmental Adaptations, and then finally revisit the idea of whether to switch Prokaryotic Structures into Protein Slots.

I can create a wiki entry to describe the system. In the meantime, since it’s not planned for this or the next release, I think we could just leave it in the “Finished Concept” bin for now and revisit it later when we want to implement it? Unless there are any inspired concept artists that want to visualize what the interface for this system will look like.

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One question I have around this is how is it visually displayed to the player what proteins AI cells have? So if you’re swimming around and you see two single hexes of thylakoids how do you work out one has a tonne of proteins and the other very few?

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It wouldn’t be displayed. Do we feel that it’s necessary that they are displayed?

Well I guess they would all look the same, but maybe that’s ok.

I guess one question is that if agents are in that same system then you wouldn’t have any ability to tell what was dangerous or not.

Which might be tricky from a gameplay perspective, and might be awesome, not sure.

Nope, you wouldn’t. There’d be an element of uncertainty when approaching foreign species as to what they’re capable of.

I’m not worried enough by it now to suggest we change that approach, I think it’s better if we just proceed like this and see how the player-base feels. I think it is important that not all information, especially about the AI players, always be immediately available to the player.