Organelle Upgrades

Okay so it’s been a long while since I last approached this topic, I believe we should try having a go at this again as it’s features may potentially be relevant for other plans. I am going to go ahead and lay out my current ideas for the upgrades system.

Part Menu:
First thing’s first; The selection menu. I believe we have a good idea on this already with the concept that Nick posted above. I think the menu would work great, and if players dont want to have to navigate it every time, we can introduce shortcuts like “Ctrl+Right click” to access features quickly which would make things more intuitive. It is here that the upgrades system will be accessed in full depth. By default, I think just left clicking on a part could work, but if that has weird conflicts with part placement functionality than we could likely make due with replacing the right click instead.

Sliders:
Next, is the upgrade system itself. I think it has been largely decided that we will basically alter the shapes of the organelles with sliders, while applying other functional changes through the use of “specialization” or whatever you want to call it.
When it comes to flat sliders versus crossgrades, I no longer have a preference. Crossgrades make it more intuitive to change the shape of the organelle, but could potentially be somewhat harder to program, and could potentially be rather wonky when the player wants to expand multiple attributes. Flat sliders will be easier, as we already have them implemented for other features, but using these will require multiple sliders for a single part which in itself might not be great.
Maybe we should construct a poll for this sometime.

Specialization:
And that brings me to specialization itself. I have two proposals on how we could do this.

Method A: Located within the Modify menu (Potentially located to the side of the modification sliders) will be a list of specializations, which will change how the part looks and/or functions. By selecting an option from this list, the player will be able to change the functionality of their part in relatively preset ways. (Example: Player clicks the toxic pilus upgrade, which replaces their pilus with the chosen type.)
This method is relatively simple, and hopefully easy to understand.

Method B: The player is presented with a list of modifiers that can be chosen and “installed” into an organelle. Some of these modifiers could reveal sliders that would permit the player to adjust their effects. The player would be able to install multiple modifiers on a part, which could allow for interesting combinations. (Example: Player clicks the length modifier, toxic pilus modifier, and straw pilus modifier. And then adjusts their pilus to be at their desired length.)
This method could be a great deal more complicated, and is somewhat harder to explain to new players. But I feel it could lead to great customization options. We would need to think carefully on how to best balance this as well. (Max modifier limits? Downsides for each modifier? Disabling conflicting modifiers?)

Upgrade Managment
I feel that with the inclusion of changes to individual parts in the player’s cell, we should make sure that it is easy to find what is modified. Parts that have been upgraded, will have icons on their hexes in the editor that will allow the player to easily identify what they have tweaked. This should make it easier to differentiate them from untouched parts.

Additionally, we could potentially include a means of copying and pasting part changes which would allow players to quickly and easily create new parts without having to go through making the same changes again.

If either of these proposed methods are accepted, we will need to begin thinking about how costs will work with this system, as well as how autoevo will utilize it.

Concept Imagery

Concept 1 showcasing the A method.

Concept for the icon tag that represents that a part has been modified.

Concept 2 depicting the alternative B method.

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It’s been some quite time now, I had been hoping to promote discussion on this topic but it seems that no one has had any additional ideas or input so I’ll go ahead and make a decision to avoid stagnation of the topic, and allow me to move on to things that depend on this topic’s full completion.

I have decided that the upgrade menu should open up as a pop-up window upon clicking the “Modify” option within the part context menu. This will allow players to be able to reference the parts list without needing to close and reopen the upgrades window.
image

Within the upgrade menu there will essentially be two types of upgrades. Upgrades that change the proportions of a part will be implemented as sliders, while upgrades that change the behavior will be selectable icons.

I personally believe and have decided that the previously proposed crossgrade sliders would look too messy, and be a hassle to implement in the presence of already existent normal sliders. If anyone disagrees please say so, I am willing to concede to popular opinion here.

Players will be able to select multiple upgrades as long as they do not conflict with others. When a selected upgrade conflicts with another, the conflicting upgrade will be greyed out until the perpetrating upgrade is removed. Players will be able to remove upgrades for a small cost of ATP. Slider upgrades should cost roughly the same as rigidity/fluidity changes in the membrane.

Modified parts will display a special icon that signified that the part has been customized, allowing players to quickly find parts they have changed.
image

This is now my present decision and plan on how we shall implement part upgrades in the future, if anyone disagrees please say so as I am always more than willing to discuss what should and needs to be changed.

Otherwise, from here on out I will now focus my efforts on planning out the types of upgrades that will be available to players, as well as the potential connections of this system to the unlocking system.

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Yeah, we can use the normal Godot sliders for, well, normal sliders. A multidimension slider selector, we would need to create a new GUI component type ourselves.

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Alright, I have come up with some rough ideas (Outside of the ones proposed by @NickTheNick) for various upgrades for the parts in Thrive. I tried to avoid anything particularly uninspiring and was hoping to provide various unique and situational changes that could allow players to further adapt to specific niches. I didn’t come up with as many as I would have liked, but it should be a decent start as we can always design new upgrades at a later time.

Upgrade Proposals

Cytoplasm:

  1. Capacity: Further devotes cytoplasm to compound storage, reducing glycolysis function in return for possessing more storage
    Glucose consumption reduced by 0.006 and ATP production reduced by 1.5 in return for +4 additional storage capacity.

Metabolosomes:

  1. Thermogenesis: Metabolosome will consume extra glucose and produce heat in return.
    Will consume 0.05 more glucose (0.042 glucose at 21% oxygen) and lowers temperature tolerance by 0.5C (EX: Temperature range of 21C-30C becomes 20.5C-29.5C)

Thylakoids:

  1. Brown Pigments: Thylakoids become specialized in harnessing blue wavelengths of light, allowing them to produce glucose in low light conditions at the cost of producing less overall glucose.
    Not actually sure how to pull this one off without custom behavior reworks, my desire is that this would be more efficient at low light levels than high light levels.

  2. Flattened: Thylakoids are now flat in shape, reducing overall mass at the expense of surface area and glucose production.
    Reduces glucose production by 0.005 glucose, and mass by 0.02.

Flagellum:

  1. Length (Slider): Length can be adjusted, changing force at the expense of ATP cost.
    I will need to take a look at how speed works behind the scenes but ideally something like +0.1 speed/-1 ATP per point in the slider.

  2. Reverse: Flagellum now operates backwards, allowing players to move forwards with front-mounted flagella.
    Does exactly as it says, makes flagella operate backwards.

Pilus:

  1. Length (Slider): Length can be adjusted, increasing the range of the player’s attacks at the expense of damage.
    Something like -1 damage/+length per point in slider.

  2. Girth (Slider): Girth can be adjusted, increasing the damage of player’s attacks at the expense of more mass.
    Something like +0.5damage/+0.02 per point in slider. Somewhat hidden benefit of having a wider hitbox, making it easier to block projectiles?

  3. Straw: Turns the pilus into a hollow tube for hostile resource transfer.
    Pilus deals 4 less damage, but now steals 0.2 of each consumable resource from target cell on hit.

  4. Toxic: The pilus now injects toxins into target cells.
    -2 damage, +2 toxic damage. Basically would allow players to bypass physical defenses in other cells by exploiting a lack in toxin resistance. Should this require toxins in storage to function?

Mitochondrion:

  1. Thermogenesis: Mitochondrion will consume extra glucose and produce heat in return.
    Will consume 0.1 more glucose (0.063 glucose at 21% oxygen) and lowers temperature tolerance by 1C (EX: Temperature range of 21C-30C becomes 20C-29C)

  2. AntioxyNT: The Mitochondrion can now assist in metabolizing toxins at the cost of less ATP generation.
    Will produce 10 less ATP, but provide 0.01 toxic resistance in return. (16.17 ATP at 21% oxygen)

Chloroplast:

  1. Brown Pigments: Chloroplasts become specialized in harnessing blue wavelengths of light, allowing them to produce glucose in low light conditions at the cost of producing less overall glucose.
    Same issue as with thylakoids.

  2. Flattened: Chloroplasts are now flat in shape, reducing overall mass at the expense of surface area and glucose production.
    Reduces glucose production by 0.02 glucose, and mass by 0.1.

Note that I specifically avoided upgrades to toxic parts for now as that was starting to get into agent-editing territory which is something we haven’t fully planned out or decided on yet.
You might also notice that I have proposed some upgrades that alter the cell’s temperature tolerance which won’t be effective until a later time.

My primary concern is that for some specialized upgrades to function, we may have to create situational code for them which might lead to a little bloat, which is something to avoid if my understanding is correct.

If anyone has anymore ideas regarding potential upgrade types, or commentary on what I myself have proposed, please say so!

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I suppose we would need to split the sunlight, into different wavelength types. That way we can have per patch composition of light, and then the different photosynthesis parts could use different wavelengths to have differing effectiveness in different parts.

So this would make the cell survive in colder environments? This would be related to: Environmental Tolerance Adaptations

Does this work currently like this in game? Or does it currently not allow front facing flagella to move the cell forwards? I have a feeling that it was like that at some point, but it may have changed.

I think it would make sense for injecting toxins to use up toxins in the player cell. And if there isn’t enough toxin to inject it would just deal reduced damage.

In a clean design, you wouldn’t really have exceptions. Instead you would have general purpose systems that support that variation. So far none of these sound like they need too much really specific functionality, though many of these depend on future features being done.

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We are approaching a point in development where upgrades might be more relevant, so here are some proposed organelle upgrades to ensure that we have material. Much of it is based on Buckly’s previous post above, and I simply included more organelles and slightly tweaked some existing concepts, which absolutely is open to comment and reversion.

I would like to spend some time in the near future on related concepts, such as refining the enzyme concept and defining gameplay themes across the prokaryotic and eukaryotic parts of the stage, so I would like to see if there is some consensus on these ideas.

Input would also be appreciated on how to sleekly demonstrate some important stats surrounding your organism, such as environmental tolerance ranges.


GENERAL NOTES - Perhaps right-clicking on a placed part only applies modifications to that specific part, but right-clicking on the part button in the editor GUI applies modifications to all future instances of that part placed.

I brought up in discussion with Buckly the idea of traditional upgrades - in other words, upgrades which outright buff a part’s process efficiency to make it better, with only the slight cost of increased ammonia/phosphate costs - and he said that in his opinion, it would be better to stick with specializations and tradeoffs. While I do think that flat upgrades should eventually be considered, as there are certain leaps in evolution in the multicellular stage which would be really difficult to represent through small-scale specialization, I do think it is a very good idea to focus much more on upgrades that come with tradeoffs as opposed to upgrades which outright make a part better; such is the epitome of evolution, and would make for the most dynamic approach to gameplay.


Metabolosomes

Anaerobic/Aerobic Toggle - A switch between an anaerobic and aerobic metabolic breakdown of glucose. Anaerobic metabolosomes produce less ATP, but are more versatile in habitable ranges. Aerobic metabolosomes produce more ATP and provide tolerance to oxygen, but are dependent on the presence of oxygen and will lose anaerobic function. (Variant; will need to consult with theory to see exactly how best to approach this)

Antitoxicity - Metabolosome assists with the metabolizing of toxins at the cost of less ATP generation. Four less ATP while providing .01 toxic resistance. (Slider)

In the previous concept, antitoxicity was a perk of mitochondria, relegated to being eukaryotic. I suggest that it might better to offer anti-toxicity to prokaryotic metabolosomes since toxins are really important amongst prokaryotes. If we want the antitoxicity slider to instead be a special “power” for eukaryotes to distinguish themselves from prokaryotes however, I’m all ears.

The anaerobic/aerobic toggle will be important in the arrival of free oxygen that will happen across most early worlds when oxygenic photosynthesis appears.

Mitochondria

Antitoxicity - Mitochondrium assists with the metabolizing of toxins at the cost of less ATP generation. 10 less ATP while providing .02 toxic resistance. (Slider)

Thermogenesis - Mitochondrium will consume extra glucose, providing heat to resist the cold in return. Will consume 0.1 more glucose (0.063 glucose at 21% oxygen) and lowers temperature tolerance by 1C (EX: Temperature range of 21C-30C becomes 20C-29C) (Slider)

Hydrogenosome - The mitochondrium will become anaerobic, allowing a wider range of habitability. However, ATP production will decrease by 50%. (Variant) Hydrogenosome - an overview | ScienceDirect Topics

Note that I suggest thermogenesis to be a unique eukaryotic capability in contrast to the previous post. Once again however, I’m not particularly pushing for this, it’s just a suggestion we can figure out through conversation.

Thylakoids

Oxygenic - Photosynthesis will now split water to produce oxygen, increasing the efficiency of photosynthesis but necessitating aerobic tolerance. 8.9B: Anoxygenic Photosynthetic Bacteria - Biology LibreTexts.

Red Pigments - Increases photosynthetic efficiency in low-lit conditions, but decreases photosynthetic efficiency in normally-lit conditions. (Slider)

Brown Pigments - Increases tolerance to cold temperatures, but decreases tolerance to higher temperatures. (Slider)

A brief google search I did seemed to indicate that red pigments were found in deep-sea photosynthetic organisms (seaweeds and other red algae) and brown pigments were found in photosynthetic organisms closer to the poles, so I wanted to reflect this to more accurately reflect life as we know it by adding red pigments and attaching Buckly’s idea to them.

The first suggestion reflects a bit of evolutionary history, where it took a while for photosynthesis to begin splitting water, and thus, producing free oxygen. It adds a cool layer I think, but it obviously can be cut if we decide that is too much detail.

Chloroplasts

Red Pigments - Increases photosynthetic efficiency in low-lit conditions, but reduces photosynthetic efficiency in normally-lit conditions. (Slider)

Brown Pigments - Increases tolerance to cold temperatures, but decreases tolerance to higher temperatures. (Slider)

Flattened - Thylakoids within the chloroplast are flattened and more streamline, reducing mass and increasing speed but decreasing glucose generation by 10% (Slider?)

Notice the lack of an Oxygenic option, which is supposed to reflect eukaryotic photosynthesis on Earth. The option can be included here as well if you guys think it is warranted.

Chemosynthesizing Proteins

Increased Tolerance to Heat - Increases tolerance to heat by .5 Celsius and decreases tolerance to cold temperatures by .5. Increases total mass by .25(?). (Slider)

Sulfur Granules - Produces sulfur granules, increasing toxin resistance by 5%. Produces 10% less glucose.(Slider)

Sulfur granules have been observed in some sulfur-respiring organisms, but I took a bit of liberty in gamifying them. Open to suggestions and comments.

Chemoplasts

Increased Tolerance to Heat - Increases tolerance to heat by 1 Celsius and decreases tolerance to cold temperatures by 1 Celsius. Increases total mass by .25 (Slider)

Sulfur Granules - Produces sulfur granules, increasing toxin resistance by 10%. Produces 10% less glucose. (Slider)

Rusticyanin

Mineralization - Creates mineralized granules which add +2 Health, but reduces ATP production by 10%. (source)
https://journals.asm.org/doi/10.1128/AEM.01492-06

Similar to the sulfur granules of the above organelles, iron granules appear in certain iron-respiring cells but their exact purpose isn’t well known, so I took some liberties in gamifying them. Again, open to comments.

Nitrogenase

Denitrification - Instead of passively generating ammonia, the nitrogenase will speed up cell processes by up to 5% depending on the amount of ammonia within the cell(?). Releases Nitrogen. Exclusively anaerobic.

I’m not 100% sure if this is solid and I just spat it out, but I want to hear thoughts. The nitrogen cycle is a very prominent component in life as we know it, both in the niches which cells take and the ecosphere’s overall health, so it feels a bit weird just having a single part of it in. I get a similar feeling with hydrogen sulfide and chemosynthesis, but of course, we should be limiting our scope in some ways.

Nitrogen-Fixating Plastid

Not so sure about this one.

Chemoreceptor

Cell-Tracing - Allows the tracking of specific cell species instead of compound clouds. (Variant)

Pilus

See Above Post

Would like to note there is potential for a lock-and-key method here, with different lengths and girths being more effective against different membranes, but we should be wary with just throwing a lot of concepts into the lock-and-key method and look at the stage holistically to make sure we aren’t overwhelming players.

Flagellum

Length - A shorter flagella decreases sprint speed but decreases the rate at which stamina depletes. A longer flagella increases sprint speed but increases the rate at which stamina depletes.


Note to the Graphics Team - I personally don’t think that there is a need for a lot of wildly different models to be created for most upgrades. I would think that most changes would take the shape of small variations. If an artist would like to spend some time discussing this, don’t be afraid to reach out or just start conceptualizing.

That sounds like even more work as that would be a separate system and it needs to be designed how that interacts with normal upgrades. I’d highly suggest we do not consider that kind of design. Only one placed organelle at a time should be able to be upgraded.

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I think these are some good ideas to start with.

When we are ready to attempt implementation, I think that focusing on the fundamental/popular parts like mitochondria and chloroplasts (and their prokaryote analogue) first will be wise. Balancing and fine-tuning this feature is gonna be pretty intensive.

I’m by no means an expert, but I personally feel that these might be either waste byproducts of lithotrophy, or some unknown mechanism that promotes oxidation from what I can understand from the journal. That being said, iron compounds being used for defensive purposes is not unheard of, at least not in the macroscopic scale. The scaley foot gastropod is a prime example of this.

We might have to consider something like it at some point if modification becomes so expansive. The problem being that with the current concept as I originally devised, you will need to manually apply upgrades to each part after you place them, which can be tedious. Hopefully it won’t be a problem.

I am admittedly rather wishy washy about this concept lately. Looking back to it after all this while, I’m starting to feel like something isn’t quite right with it. I’ve found myself in a mental mess of part variants, modification menus, and protein customization that is just not coming together. For example I’m starting to feel that upgrades like the hydrogenosome could be categorized as a “variant” which could be swapped out to replace the mitochondria or vice-versa or something. Changes like thermogenesis could be overarching modifications a la protein slots of old.

Alas It’s a big mess and I don’t really want to keep redesigning this over and over in an endless loop… So don’t mind me.

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You’re right in regard to the iron-as-byproduct comment. It is indeed a waste product of lithotrophic metabolic processes. And also, I do advocate for having something like a hydrogenosome be a variant.

And I understand where a lot of this feeling of “mess” can come from. Atleast for me, it comes with realizing there are multiple concepts, like the protein enzymes concept and organelle modifications, that can deal with similar facets of the game, like environmental tolerances. It’s definitely a lot to deal with and wrap your head around, and there’s a lot of pressure to get it right in a way that is incredibly detailed and widely applicable at the same time.

Some food for thought and perhaps you might agree with this line of reason: I think environmental tolerance adaptations in the microbe/early-multicellular stage will mostly be dealt with through the enzyme system, and will transition to modifications as the player’s organism gets more advanced and larger. In my head, environmental tolerances granted by protein enzymes have reduced effect as your organism’s mass increases. So as a prokaryote, those enzymes make it so you don’t need to go through modifications, or atleast only small modifications, but as you get larger, those enzymes will reduce in their power, hence necessitating more morphology based adaptations. I think such an idea is good because…

  1. This reflects real life, where unicellular cells can adapt rather well to their environment through enzymes but multicellular organisms must rely on morphology so that their various cells are all optimally functioning.

  2. Makes it so that enzymes can’t just carry the player’s evolutionary burden the entire way regarding environmental tolerances, forcing them to deal with morphology.

Besides that suggestion, it’s also important to keep in mind that it isn’t all or nothing; we don’t have to get it perfect in the first try, and likely won’t. Like you said, this will require a lot of balancing, so it very much is a multi-step process that allows us to stop, zoom out, and assess from time to time.