Passive Enzyme/Protein Slots System

For quite a time now, there have been ideas and concepts about a potential protein slot system floating around these forums. I personally always liked the idea it represented and decided that it finally needed it’s own place to call home on the forums where we can discuss the concept directly without sidetracking the discussions it arose from.

I believe the original concept was devised by Tjwhale(?) who mentioned a slot system where players would insert a protein from a selection into a set amount of slots inside their cell as an alternative to placing the proteins as physical parts. The only limitation to this system being that the slots are limited in quantity. There were not any concrete plans as to how players would increase the amount but some ideas included adding more nuclei to your cell, or simply having more slots as your cell gets bigger in size.

Here, I have devised my own concept of such a system, but rather than having a hard limit of slots, I have each type protein taking up a different amount of space in the cell’s “genome”.


This allows players to intelligently sort and place their proteins with a more fun and soft limit to the amount they can have, while still keeping with the theme of a slots system. The size of each protein can be variable, meaning that through an upgrades system players could potentially adjust the size at the cost or benefit of protein efficiency. That way if players wanted to have a really good cold resistance, they would need to sacrifice a lot of room they could have used for other proteins. Similar to previous concepts, I would like for the nucleus to increase your cell’s protein capacity.

These proteins will have a purely passive effect on your cell, rather than providing any active features. effects will probably include temperature resistances, toxic resistances, faster healing, etc. I would really like to have some more complex features if it’s possible and introduce things such as proteins that adjust your cell’s need for oxygen or other gasses, so long as there are real life counterparts. This system could potentially make a great home for more active compounds such as binding agents however, so I’m willing to discuss that matter.

Edit: After going over this post again I have noticed that it’s possible I may have created confusion as to the intention of this concept. I should mention that this concept was not originally devised to replace the prokaryotic protein parts, but to instead provide a method of adding passive effects and bonuses to a cell without physically making the cell larger in size. That is, it was intended to be a system alongside the placable parts.

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It’s a nice idea.

A couple of things that could be considered.

It’s possible to have proteins as single hexes which are placed in the normal cell. The soft cap then applies that adding them makes your cell bigger and slower and take more energy. This is very easy to fit with the current system. However this is very unrealistic which might put people off.

With your system above it could also be hex based with each protein taking 1,2 or 3 hexes of space in a finite line or grid of hexes. This has the advantage of again fitting with the established hex based interface. However it has the downside that the variation in cost for the different proteins is limited to these integer values whereas yours is nice because it’s continuous.

Anyway yeah I don’t mind in any direction particularly. Nice idea, looking forward to seeing what it turns into. :slight_smile:

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Really cool idea. I’ve been thinking a lot about this, organelle upgrades, (potentially) organelle unlocks, and agents, and how they could all mesh together.

I really like how this system gives an easy way to balance powerful genes with few drawbacks, by making them take up a lot of gene space. It also gives a function to the nucleolus, nucleus, conjugal nuclei, and multinucleus by making them add more gene space. Plus, with organelle upgrades, that could allow for the different types of nuclei to be upgraded to offer more gene space. Something cool about this is that it parallels the idea for the Society Stage where you have “Knowledge Space” which can be increased by building and upgrading your libraries. And to top it off, I think this would be a perfect system for evolving agents as well, which would also take up gene space. It would be a nice all-encompassing system.

This also makes me think about the Prokaryotic Organelles, as TJ noted. I know we originally decided to make prokaryotic “organelles” placed as hexes, but if we do like this “Genome Space” system I would consider removing the prokaryotic organelles as hexes and instead implement them in this system. After all, they are just proteins themselves, and it would be more accurate if they were implemented in the same way as the other proteins. Additionally, it would be more realistic too, as these proteins are too small to see at the cellular level and would not show up visibly in the cell as other organelles do. I know its frustrating to renege on an old decision, especially since I remember being one of the ones who supported hex placed proteins back in the day. But I do really like this Gene Space system.

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I guess the drawback to this is that all the cells would then look the same? I mean aren’t we then basically ripping out most of the hex based editor gameplay at that point?

Moreover wouldn’t the gameplay still be the same, you add things from a menu to a grid or box, but we’re just remaking it slightly differently in the name of improved realism?

That feels like a lot of work and I’m not sure about the payoff.

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I’m glad you really like it! Though I would like to point out that I am somewhat hesitant about the idea of using the system to entirely replace the prokaryotic parts. The big reason for this is that it may feel really abrupt and jarring to switch from mostly configuring your cell with this system, to largely building your cell with parts upon getting your nucleus. I suppose we would still have a few prokaryotic parts but it would be quite limited.

I’m not entirely against that idea of course, it’s just a large change to how Thrive currently works so we need to think carefully on how we would want to go about that to make sure it’s seamless and worth it.

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Yeah the drawbacks would be less visual differences between prokaryotes, as well as less hex placement interaction in the prokaryotic phase of the Microbe Stage. I’m thinking the benefits would be that prokaryotes could stay smaller while adding these proteins, make prokaryotes look a little more realistic, and would be a little more elegant since all proteins and agents are handled in this one same system.

But yeah, it would be a big change, so I’m not 100% convinced on it, and I think we’d definitely have to consider whether it’s what we want to do.

But on a separate note, I think this gene space system could be a really cool system if we decide to go with it.

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I had this idea lingering on my head for a while and i finally made a concept for it. I think proteins should be placed on the membrane instead of inside the cell. They would occupy a certain area, maybe the whole membrane, though that could have some drawbacks like decreased absorption speed.
The surface percentage these proteins occupy would be controlled with sliders in another editor tab and once the player evolves new proteins these could be added to the membrane. However they would share the cell’s surface, so adding too many different proteins would make the cell less efficient, albeit it would have many different processes. This could be a solution to organelle gluttony, at least for prokaryotes.

If the player wants more processes then they can add more cytoplasm as usual, increasing the size of their cell and also the surface available for more proteins, i guess it would come to a point where this strategy would become inefficient (square cube law ftw!) and the player may want to either improve their proteins or become an eukaryote.

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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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