Organelle Upgrades Discussion

Future Game Microbe Stage
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Similar to the Cool Cell Behaviors Thread, this topic is meant to be a discussion regarding organelle upgrades. If you have ideas regarding how different organelle upgrades could work, don’t be afraid to post.

At the same time, if you heard of a cool microbial feature in real life that would be interesting to be implemented in Thrive as an upgrade but are not really sure as to how said feature would be implemented, still bring it up; we can help you figure it out.

Here are a couple of examples.

@The_Void suggested filter feeding, which he envisioned would be represented through a cilia upgrade. You would simply press a button which would basically create a vortex around you that sucks potential food items towards you, at the cost of burning ATP.

Caulobacter
Some cells are able to use glucose to generate a sticky substance akin to glue which slows down cells around them. I think this could be implemented through an upgrade to oxy-toxy, which basically makes the effect of a toxin projectile slow you down instead of deal major damage. It would be very cool to see once toxins are treated as compound clouds.
https://www.nature.com/news/2006/060410/full/news060410-1.html

Geo-electric
Some cells are able to use natural compounds such as Iron to generate enough electricity to provide them energy. I believe this could be implemented in Thrive through an upgrade to the mitochondria/metabolosome, in which absorbing the iron compound would basically increase the efficiency of those organelles.

I also have an idea regarding how upgrades to the flagella/cilia could work. It would be based on altering the length of the organelles.

Basically, increasing the length of cilia/flagella would increase the maximum speed your cell could generate, at the expense of agility/acceleration. For example, if you increase the length of your flagella, your maximum speed would increase rapidly at the cost of a hit to your ability to turn and rapidly accelerate. If you shorten it, your maximum speed would decrease (less severely than it increases when lengthening), although turn rate and acceleration would be noticeably improved. I would suggest that flagella using organisms could only move the way opposite to the force generated by the flagella.

Increasing the length of your cilia would increase your speed and impact your acceleration and agility; however, the effects of this lengthening would be less severe than the effects of lengthening flagella so that there is much less overlap in functions. Shortening your integument would reduced your speed but seriously improve your agility/acceleration, to the point at which you can rapidly change direction.

I believe this would introduce an interesting dynamic to cell movement/specialization.

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Check the dev wiki, the original plan was to have a lot of different agents, which would have various effects, from direct damage to organelle inhibition to slowing down to communication agents. In this thread I put the table from the wiki, which, while outdated, should still give a good idea.

There’s this image from the dev forums a while back, your idea was basically the plan, but including thickness. image

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Although the ideas of each toxin are pretty cool, I’m wary of having the toxin system simply be a huge list of different toxins with a lot of specific effects on specific organelles; or atleast, if that is implemented, we need to do a really good job balancing to make sure that toxins don’t make other toxins redundant. For example, why would the player want to specialize their toxin to specifically attack mitochondria, chloroplasts, flagella, etc. when there is a toxin which attacks a feature that every cell is guaranteed to have: cell membranes? A lot of the toxins in that list, such as carbonate and organelle digestor, are also pretty broad and have entire concepts attached to them, so I don’t think it would be a wise idea to base gameplay concepts on the wiki page.

That’s a really good thread to revive however, as development seems to be beginning to shift towards developing organelles and the idea remains pretty vague.

And nice catch for the flagellum upgrade concept. One gripe I have with it however is the whole increasing ATP consumption as length increases; I feel that that’s basically the same as putting down another flagella. I think it would be wiser to make it so that editing movement organelles simply alters the way your cell moves, not the consumption stats of how it moves.

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I dont know what organelle this would be an upgrade from, but an ability to attach yourself to an iron particle or other large objects could be made. This would mean not having to spend any ATP for movement, but would lead to a stationary lifestyle, like of a plant.

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As always, the developers should look to nature for guidance when in doubt. There must be some reason why a sperm, for example, has one big flagellum instead of many small ones. The real advantages or disadvantages of that could then be reflected in the game. I hope that the developers totally avoid the game design of Paradox, where the game has numerous arbitrary currencies that are added or removed. That feels very gamey and (I write it again for emphasis) arbitrary. Do you remember when Alexander the Great tried to conquer Persia but couldn’t because the provinces cost too much warscore and he didn’t have enough administrative mana to core them? No, you don’t, because reality was not restricted by these arbitrary numbers.

For organelle upgrades, I think one should study what is known about how organelles evolved and which ones evolved from which previous ones. I am not familiar with the topic, however, so my present usefulness in that regard is nil. In any case, the upgrades should be kept within reason. The player should not be able to evolve a super-mitochondrion that is more efficient than any real mitochondrion. I also prefer things be dynamic instead of scripted. As such, I think having a specific organelle called a flagellum is less ideal than being able to morph the cytoplasm and build a flagellum from simpler parts. The player could start by ruffling the cytoplasm to make cilia and then make the cilia larger and fewer until only one remained, a flagellum. I do not know, however, whether that idea is feasible in the context of Thrive.

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Some time ago I made this post regarding organelle upgrades and though it is not perfect, I think that with some tweaks it might be something we might discuss.

A lot of parts there really need some kind of fixing/balancing, but I hope we can figure that out. I cannot wait for your feedback. As always, lemme know whatcha think. Thank you!

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Although definitely a cool idea, because a stationary game plan isn’t exactly the most fun, its integration should be limited. I could definitely see this being a behavior trait which effects other members of your (or another) species, which increases their auto-evo stats if said cell was able to use iron as energy.

Agreed. New game mechanics should be implemented only because they either represent a concept of evolution effectively or are fun/beneficial to the overall play-through. I think that hard limits should be kept to a minimum unless it is absolutely necessary to introduce one due to an interest in balancing a game mechanic, and that the biggest obstacle which limits the player should be the total energy their organism is able to produce which is accentuated by concepts such as the square-cube law. Thus, the player’s own and other species would evolve realistically, somewhat guided by the same evolutionary pressures which directed Earth organism’s evolution; develop your beneficial parts into something even more efficient and ditch the parts which make you spend more energy than what is needed.

Beautifully said. I think upgrading organelles should be an important part of unlocking newer organelles as well in order to simulate the linearity of physiological traits.

@Zahyyy, I was actually thinking of posting my ideas regarding how organelles could derive from other organelles, but it seems that both you and I have really similar ideas! I do agree that there needs to be some balancing and re-structuring, but overall, the progression is pretty sound.

The vacoules concept sounds really good to me.

Despite how odd this might sound, no prokaryotes actually have cilia. While eukaryotes are able to have both cilia and flagella (have both as in different eukaryote species can have either flagella or cilia), prokaryotes only have flagellum. The hairlike appendages you typically see on bacteria are actually pili, which are used to attach to objects. I also think flagella and cilia don’t typically go together in the same species due to their functions essentially cancelling out each other’s effects to a certain extent, meaning the cell would be better off reducing energy spent on cilia/flagella depending on its needs rather than having both (I’m not 100% sure about this past sentence, so further research/commentary would be appreciated). So we should focus on refining that. I may have a few ideas, I just need some time to refine them.

About the toxin vacoules, the idea sounds good. I do think that prokaryotes should have some range of variability offered to them, but eukaryotes should have even more options.

Is there a reason you have the pilus derived from the flagella? I think a membrane unlock should be what unlocks the predatory pilus, as it seems likely that this feature is pretty much a hardened pili.

Endosymbiosis is an interesting problem. I have a tiny bit of a problem with having it solely be based on the integration of another cell inside your own, as that puts a huge amount of autonomy away from the player and into the hands of the simulation itself; as in, it could potentially screw over the player if the bacteria which they engulf has limited room for improvement in terms of its energy efficiency. So, I like how you have an option to let the player simply develop chemosynthisizing proteins into various energy efficient organelles themselves, which is the insurance policy I think is somewhat needed to make sure the player isn’t screwed before they even begin to transcend into the multicellular stage.

I think where engulfment of other cells (endosymbiosis) could come in is having some unlocks which increase the efficiency of your energy-producing organelles be based on consuming a certain number of microbes which use that same form of energy. I think further discussion could nail down a cool concept which makes sure that both the player is largely in control of their fate and endosymbiosis is integrated in an interesting, fun, and realistic way.

So in summary: I agree with most of what you suggested with some minor finetuning which I believe increases the fun/balancing/realism of the game. Further discussion should focus on flagella/cilia development and endosymbiosis.

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Thanks for the feedback!

I had no idea about this, thanks for clarifying. This would probably mean that flagella and cilia would not be a part of the same “upgrade progression”, but rather their separate organelles.

I’m not really sure how pili evolved, so any flaws in my reasoning should be fixed by someone more knowledgeable in biology, like you.

That’s true and I did not realize that. I think that endosymbiosis should be included in the game, as it’s such a crucial part of the evolution of life, but you’re right that this might not be the correct way of doing it.

I’m not a huge fan of this idea, but we don’t really have any perfect ideas regarding the endosymbiosis as of now.

I absolutely agree. Those areas are the least fleshed out ones. Along with the balancing and some tweaks here and there. Once again, thank you for your feedback and expansion upon my idea!

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IIRC pilii were just hardened flagella, so you’d get them through upgrading the flagellum. This’d even make sense from a gameplay perspective, since fast hunter that’d want a pilii would probably already have upgraded flagella, and not a strong, tanky membrane.

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I don’t think that predatory pilus necessarily came from flagella, but both flagella and pilus are derived from analogous structures.

I kind of tidied up up the discussion regarding movement organelles. Most of this is just the merging of many previous ideas regarding different aspects of cilia/flagella into one cohesive system.

Flagella

  • “Tail” which propels a cell forward. Can also provide sensory information
  • Can be found in both prokaryotes and eukaryotes.
  • Likely emerged via evolution from a structure projecting from the membrane.

Cilia

  • Miniature hair-like protrusions from membrane. As well as motion, used for sensing and filtering. Very diverse uses.
  • Eukaryotes only.
  • “Combs” the water around it, which can be used to generate motion.

Upgrading/Obtaining

In real evolution, the flagella was likely derived from a structure on the membrane of prokaryotic cells. Although unlocking the organelle through upgrades to the membrane seems like a cool idea, because of how essential a flagella would likely be to most movement, hiding the organelle behind unlocks which may or may not be useful to the player could handicap a player’s experience. Since the flagella was likely evolved independently across multiple instances, I think it’s a good idea just to have the flagella be an organelle available to you from the get-go.

Upgrading the flagella seems to be a largely defined concept. Here is my spin on how editing it would function:

Length

Increasing = + Maximum Speed, - Turning Speed

Decreasing = - Maximum Speed, + Turning Speed

Thickness

Increasing = - Endurance, + Acceleration

Decreasing = + Endurance, - Acceleration

image

I suggest that cells which have the flagella are largely locked to moving the way they are facing – or atleast, move really slowly when going sideways or backwards - to differentiate its movement from cilia, which I think should use the traditional WASD movement scheme.

Note that endurance/acceleration functions the same as the older flagellum concept regarding thickness; endurance indicates how long the cell moves at a certain speed while acceleration indicates how rapidly the cell reaches its maximum speed. I didn’t really want to include

Besides editing the characteristics of the flagella, other upgrades could focus on reducing the ATP cost of flagella, or unlocking sensory functions which could enhance a certain aspect of gameplay. I saw that there are concepts for various different types of flagella, so upgrades could also focus on unlocking different varieties.

Cilia are largely structurally identical to eukaryotic flagella, so unlocking cilia could be achieved via an upgrade to the flagella which becomes available after you place a nucleus on your cell. As far as I’m aware, there aren’t really any eukaryote cells which have both flagella and cilia, as they both serve a similar function and both consume considerable energy. To reflect this, I think that the energy cost of having both flagella and cilia should outweigh the benefits to maneuverability which cilia gives you if you already have the flagella.

Editing the cilia:

Length

Increasing = + Speed, - Agility

Decreasing = - Speed, + Agility

Note that there is as little overlap between cilia and flagella as possible. In other words, the most maneuverable flagella would find it difficult to match the least maneuverable cilia, and the fastest cilia would find it difficult to keep up with the slowest flagella.

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I like that idea. I also like the organelle upgrades being on an X-Y grid. That makes them both easy to calculate (as positions on the axes have specific numerical values), understand, and compare. Your ideas for the cilia and flagella make sense to me.

However, the energy budget of the game at the moment makes all of this quite moot. As the game is, there is no need to be energy-efficient at all, as a few chloroplasts and mitochondria in the tidepool mean that you always have plenty of ATP and glucose. So, before orgenelle upgrades are added, I think a reason to upgrade should be added. If my cell’s organelles are fine as they are, then I would only upgrade them for fun, not because I need to. In Kerbal Space Program, better engines are necessary to reach higher altitudes, so upgrades is necessary. That should be the case in Thrive too.

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Is there any reason why cilia couldn’t be used on prokaryotes, or is it just a coincidence that they never evolved them? If there’s no specific reason prokaryotes in Thrive should be allowed to have cilia.

I feel like this is more an issue with chloroplasts than with organelle upgrading. Chloroplasts should be nerfed as they currently produce a ridiculous amount of energy. Not only does it make organelle upgrades unnecessary, but it also creates situations which don’t make sense, like plants being more mobile on average than heterotrophs.

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I tried looking this up, and, well, predatory pili basically don’t exist. The only things I could find even the term was for sexual purposes, as an anchor, to walls and other cells alike, (so still as weapon, just in a different way)
or for sensory purposes. I’m likely missing something, due to me not being a microbiologist, but it’s still odd how when you look up terms like ‘pilus’ with ‘predatorial’ and the like, the first image you get is concept art from the dev forums.

Evolutionary speaking, the flagellum took a long-ass time to develop to it’s current efficiency. It’s ridiculously complicated, and for a lot of the proteins in it, removal means a massive reduction in the flagellum’s usefulness. Because of this, you could probably give the player access to a ‘protoflagellum’ or something which would be way less fast and burn through ATP like crazy, forcing the player to try to find a more efficient form of locomotion after a while. (At first when you start there’d still be the primordial soup of course, making it not difficult at all to find various sources of energy.)

IIRC wasn’t the flagellum likely a unique mutation due to it’s ridiculous complexity, even in it’s protoform, even being used as argument for irreducible complexity?

Also, minor thing: It’s either ‘the flagellum’ or ‘flagella’. Never ‘the flagella’. Ree.

Prokaryotic cells use pili as a sort of legs, which they can use to grab surfaces with and then pull themselves forward, but I don’t see any other reason why they can’t have cilia. I think the only reason is that the first cell to evolve cilia was already eukaryotic, so there was not chance for prokaryotic cells to split off with the same mutation.

I personally think they may not have to produce less, but instead they’d be made really heavy. This would mimic the ‘natural nerf’ they already have IRL.

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I think this is the biggest gameplay issue which Thrive currently faces. At this point, because of how hard it is to properly harness glucose after it fades from the primordial soup, there is absolutely no reason why the player wouldn’t add chloroplasts; otherwise, you will basically instantly burn through the glucose stores you spawn with, and after that, there is basically no means to replenish it.

In biology, gluconeogenesis is a function that many predatory cells have which basically turns compounds such as protein and fats into glucose through certain catabolic reactions. So, I think slain cells should drop glucose in order to encourage predation and non-autotrophic gameplay. Upgrades could also help with this. If metabolic organelles are made to process glucose more efficiently, glucose supplies can last longer, hence leading to greater motivation to become heterotrophic.

@Omicron explained it pretty well. I also think because of their size, prokaryotes had less pressure to develop an extremely motile form of movement since they don’t have a lot of mass, and thus don’t need to spend so much energy to move this mass in various directions quickly. This could be reflected in the game a tiny bit by having the player question whether or not they want to dedicate energy to a movement scheme their size already somewhat encourages, but considering the sensory functions of cilia, the organelle can be used for various functions. So yeah, I think prokaryotes should be allowed to have cilia as well.

Yeah, I’m also pretty sure that the developers took some liberties in the predatorial pili’s implementation. I’m pretty sure that real-world pili and flagella do come from a common ancestor though.

That sounds pretty good to me.

I’m pretty sure while flagella are indeed very complex wonders of nature, many proteins/components of flagella already existed/had functions in the cell prior to the organelle’s development. See:

Apologies!

I think a combination of the two effects would be really effective/realistic. Most chloroplast containing organisms are either sessile or very slow because chloroplasts don’t generate enough energy to sustain efficient movement, so it needs to be made clear to the player that choosing a chloroplast = a very slow existence.

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I know this has been discussed already, but I want to speak about upgrades and proteins.
As you know, all lifeforms have to use catalysts to make their metabolism faster. For each organelle process, there would be a base catalyst (no upgrade) and then three unlockable catalysts. Each of them can improve a process either in its own way (standard catalyst) or simply overwrite a previous one if necessary (catalyst upgrade).

For example:

Organelle Catalyst Effect
Cytosol (or cytoplasm) Base catalyst None
Mitochondrion Catalyst A, Catalyst B, Catalyst C Decrease glucose usage by 3, Increase ATP by 4, Makes anti-toxin for the mitochondrion
Chloroplast Catalyst 1, Catalyst 2 Decreases luminosity required by 1 (unused), Decreases luminosity required by 4 (overwrites the first effect)
With such a system, the devs could use the old processes while tweaking them a bit (to make the catalyst upgrade worth a while). More precisely, we can come back to this respiration process:

C6H12O6 + 6 O2 —> 6 CO2 + 6 H<2>O + 32 ATP

Of course, we can’t have 32 ATP directly from the beginning of the game; it’d be too easy. Catalyst upgrades can achieve this after you unlock them.

There are two issues, however:

  1. How do we unlock the catalysts? It could be done by a mutation in our reality, but how can we translate this into the game? We need to develop a protein system in the game.
  2. I think that some players such as Omicron wouldn’t like the idea, because they would find late-stage too easy, just like in XCOM games.
Let’s breakdown aerobic respiration into its steps.
  1. Glycolysis
  2. Oxidative decarboxylation of pyruvate
  3. Krebs cycle

Glycolysis

Overall reaction:

Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 Pyruvates + 2 NADH + 2 H+ + 2 ATP + 2 H2O

List of notable enzymes in this process:

  • Hexokinase: Phosphorylates glucose and restricts its use to specific processes.
  • Glucose-6-phosphate isomerase (GPI): Turns glucose-6-phosphate into fructose-6-phosphate. It also has a use in neurons, which could be used in Aware stage.
  • Phosphofructokinase 1 (PFK-1): Converts fructose-6-phosphate into fructose 1,6-biphosphate and ADP. It also regulates the glycolysis rate depending on the cell’s need.
  • Phosphoglycerate kinase (PGK 1): Produces 1 ATP.
  • Enolase: Produces water.
  • Pyruvate kinase: Produce 2 Pyruvates and 1 ATP.

Ideas:

  • Hexokinase could be used to change process priorities related to the usage of glucose (to be discussed).
  • PFK-1 would regulate ATP production or usage (to be discussed).
  • PGK 1 and Pyruvate kinase upgrades would increase ATP production from let’s say 1.0 to 2.5 per second (in multiple upgrades).
  • Enolase would change the quantity of water in the environment (to be discussed).

Pyruvate decarboxylation

Overall reaction:

1 Pyruvate + 1 NAD+ + CoA → 1 Acetyl-CoA + NADH + CO2 + H+

There is only one enzyme used from what it seems. It is called the pyruvate dehydrogenase complex (PDC). It doesn’t seem to have a potential upgrade. As for the product acetyl-CoA, it is said that it can be obtained by the breakdown of glucose (glycolysis) and by the breakdown of fatty acids (beta-oxidation). Therefore, maybe there could be an upgrade for PDC to include fatty acids as a second resource for aerobic respiration. That would bring that compound back into the game while giving it the first use to test.
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