Organelles / Mutations

#1

I think it would be good to make some progress with understanding which organelles we’re going to have and how they are going to work in the game.

As a decision: we’re going to delay organelle upgrades. Lets sort out which organelles we want and get them in the game with models and play with them. Then we can decide as a team if we want upgrades or not. If the game is very complicated already then we don’t want to go overboard however upgrades could also be fun.

To discuss in this thread:

Here is @NickTheNick 's list of organelles / mutations. I think it’s really strong on realism, which is great.

Re proteins, what do you think? Should we:

A. Have all changes you make to your cell be a placeable set of hexes. So if you want anti-freeze proteins you have to place them as a hex in your cell. This is a bit less realistic I imagine but makes everything the same, to change your cell you add or subtract hexes. Moreover it balances proteins because they’ll make you slower and larger.

B. Give the nucleus a certain amount of slots, maybe 4, in which you can load a protein. So from a list of 9-10 you can choose 4. This gives a good incentive to get a nucleus, it also is an interesting choice when choosing additional agent resistance vs heat resistance, for example. It balances proteins, because putting one in means leaving another one out. It may also be more realistic.

One thing in favor of slots is that they are easy to implement. Each protein needs an icon and a description and that’s about it. So it will help with quickly building out the functionality as we don’t need to make more models for the hexes.

C. Do you have another idea for how to get proteins in to the editor?

Something I am against is having proteins be upgrades without drawbacks. Like if your nucleus had 20 slots, for example, every cell in the game would use all proteins, there’d be no reason not to have all of them. I think this reduces diversity and is not interesting for the player, as getting all the proteins just means grinding MP and I am really against grind.

Re specific organelles:

In the DNA section, for now, lets have a single nucleus / nucleic core which cells either have or they don’t. We can then talk about splitting it up into multiple pieces / levels as part of the upgrades discussion and talk about things like increased “brain power” as @andross was suggesting.

Directed Cilia: What does it do that helps the player? Is there a gameplay function for it to have?

Pilli: I liked @Atrox 's image here for several different types. What do you all think of those ideas?

Contractile fibers: they sound like an upgrade to pseudopodic movement, how would they be added? Are they a single hex or a protein or something else? It’s worth managing our expectations around pseudopodic movement, we’ll have to see what the membrane system can handle. I love the idea of amoeba and there are technical challenges in this direction.

Fused cell wall: I’m not sure I understand how two daughter cells can stay fused together and then reproduce. How is this differentiated from adhesion proteins?

Microvilli: how does this help the player? If this is a lot of work to change the membrane then it might be quite a lot of work to implement so it’s only worth doing if it’s really a good adaptation.

Fat Granule: Does this function differently from a vacuole? If I can store ammonia + phosphates what benefit is it to store fat instead? Does it make sense to save this organelle for the multicellular as a way of specializing cells as storage?

Lysosomes: What do they do in gameplay terms? Would 5% reduction in compounds needed for reproduction as you can process food more efficiently work?

Peroxisomes: Does 5% agent resistance sound cool?

Eyespot: I really like eyespot. I wondered if it could be directional? So if you point it at the edge of the screen and there is a lightspot off the screen then the edge glows, as is suggested in this thread. That way it’s an active gameplay thing where you have to spin around to find the light.

Nitogenase: Presumably it makes ammonia from N2, is that right? If so it could be an organelle which just gives a small flow of ammonia. Would make sense if it upgraded into a nitrogen fixing plastid.

Aerobic / Photosynthetic proteins: I liked the idea for these as precursors to chloroplasts and mitochondria and I liked @Narotiza 's designs.

If we went with slots in the nucleus then does it make sense to have Nitogenase and Aerobic and Photosyntheic proteins be hexes (so that small prokaryotes can use them) and have the other proteins go in the slots in the nucleus?

Tannosome: what gameplay effect does this have? Could be a protein? Could be a counter to the straw pilus, as in if another cell harvests some of your compounds they get damaged? I think if it hurts cells after they’ve engulfed you then no one will use it because it’s too late. It’s like trying to collect on your own life insurance.

Also something that would be great as a team activity would be to look for other organelles that exist on earth which we haven’t considered yet. For example the eyespot is really cool and if we can find anything else like that that gives us loads of strength. I had a lookhere but there wasn’t anything that promising I don’t think. @rastro I wondered if you might be good at this.

Something to add to the list would be acid resistance protein, as @NickTheNick suggested in the acid discussion. Does anyone else have organelles they would like to add?

#2

If we go with this option would players be expected to take 4 different proteins or would there be reason to specialize and take 4 of the same? I personally like option A at least for now because it allows prokaryotes to access proteins and doesn’t require any work except for coming up with a model and deciding what exactly they do.

I thought the idea here was less thrust more torque (Just like in Spore)

Stab, injection, and straw pilus all seem like they could be very high on the awesome scale. Would we have these be 3 different things though? Once you unlock pilus you can use it as stab, if you also have a toxin then you can choose to either buy a stab or injection pilus (Naturally injection is more pricey). What would be the requirement for a straw? Combining with a vacuole?

If we can have a vision cone that depends on eyespot placement and cell orientation that would be awesome and could lead to some interesting things later down the road. Will predators keep their eyes forward and prey more to the sides like on Earth? It’s a very good idea.

You suggested with the removal of O2 and CO2 that we for now just take them to be some fixed environmental value and then in the future have the vary from biome to biome right? Naturally nitrogen would be in the same boat. It’s not something that should be spawned in a cloud but it should be an environmental factor that will increase or decrease the efficiency of these processes.

#3

Lots of great points and questions.

I think Directed Cilia are different than Motility Cilia in Nick’s list and I’m interested in what Directed Cilia might do in gameplay terms.

#4

Realistically each active protein would need ATP and compounds for it to be generated. This could even extend to allow the player to tweak how much of each protein they want to make, so they could have a bit of resistance against all toxins, for example, instead of having to choose just a few that they are fully resistant against.

#5

I think Option B is the best approach because it balances realism with gameplay well. Realistically these proteins would be so tiny that the cells would still be able to stay small. The drawbacks of the proteins would be that they increase your ATP usage and reproduction cost (extra ammonia is needed to reproduce), and if we go with the nucleus slots idea that could be another way of limiting proteins. However, if we go the nucleus limiting approach I don’t think the nucleus should be a requirement, because many of these proteins are available for prokaryotes, I think it’s better if the nucleus just expands how many you could maintain (either through a soft or hard cap).

This refers to cilia that beat in a pattern to bring compounds into a “mouth” region of the cell, so typically a player would place two sets on either side of a region of blank membrane to draw food into the membrane.

I was thinking that Contractile Fibers could allow a cell using pseudopodia to extend larger pseudopods, or extend and contract them more quickly. Visually we might be able to show this via striations in the texture of the cell (showing the fibers in the membrane). It would be a mutation that encompasses the entire cell. Also a cool effect of this organelle is that it gives a really good segue into the Multicellular Stage, because cells that evolve Contractile Fibers would become muscle cells in the colony.

In this case imagine the cells are contained within a shared exterior cell wall, even though the two cells are both separate with their own membranes. Every time a new cell is born it would be trapped inside this shared cell wall. I’m not sure what the gameplay implications of this mutation would be though.

This would greatly increase the surface area of a segment of a cell’s membrane, allowing it to much more quickly absorb and release compounds (one of the biggest limiting factors of eukaryotic cells). It carries well into the multicellular stage because this would be the kind of mutation you’d want on, for example, absorptive cells that collect food.

This one I’m not really sure how we could integrate into microbe gameplay, since it just does the same things as a vacuole, but it’s kind of a shame since it’s a useful organelle. Maybe we don’t even need the fat granule organelle, a fat cell could just be a cell with a giant vacuole in its membrane.

For lysosomes the plan was if the player engulfs large particles (not compound clouds) like floating proteins, organelles, or entire other cells, they’d normally only be able to harvest about 30-40% of the compounds (the numbers aren’t final), while the rest get lost to the environment from the inefficiency of the digestion. However, with lysosomes, you’d be able to harvest about 70-80% of the compounds from these large particles, making the digestion a lot more efficient. This would carry well into multicellular because a player would want to place lots of lysosomes in the center of his colony where the digestive cells are.

For this one I’m not very sure if it’s worth adding, since it doesn’t seem to have any primary functions. That idea could work though. Maybe it could just be like a general agent resistance organelle, or maybe it’s better to just handle agent resistance via the Nucleic Core and leave out peroxisomes.

Yes and yes.

I’m not really sure, I put that in because it was mentioned on an old thread but I’m not sure if it’s worth adding. In fact from doing some quick reading right now it seems that tannosomes refer to vacuoles that store a toxic agent called tannin, so technically this is already covered under the agent system (similar to druse, where the cell can produce and store toxic agents to ward off predators).

Ah good point, I’d forgotten to add that one. I’ll go through and make sure to add in any of the other ones I’d forgotten soon.

#6

Great.

Couple of questions:

So currently I guess cells can absorb things anywhere on their membrane.

With Directed Cilia moving things towards a “mouth region” what is the gameplay advantage of that? Why would I want to move things to a certain region of my cell? If this is going to be a gameplay feature I think it’s needs a bit more fleshing out, though a “mouth” sounds like it could be cool.

The way I’ve been imagining it is that in the 2D multi cellular a player will specialise their cells for different functions by adding organelles to them. So for example you could add a fat granule to a cell to make it a fat storage cell which would allow you to place fat tissue on your creature. Is this what everyone else is thinking?

Of the organelles above as you are saying they fit naturally into the multicellular is it worth saving them for that part of the game? For example: fat granules, contractile fibers (to specialise muscle) and microvilli (to specialise gut cells) and maybe some sort of calcium organelle for specialising bones could be introduced then to allow this specialisation? What do you think? Is it worth saving some of these for this part of the game?

If they’re going to be in the microbe stage they need gameplay reasons to be there. So if you put microvilli on you need some kind of bonus and some kind of drawback.

#7

I prefer option A for the proteins because prokaryotes don’t have nuclei, so the system would have to be completely different for them, which adds more division between eukaryotes and prokaryotes, which I think we’re trying to avoid.

#8

Actually now that Naro mentions that I think I’m for option A as well. I just remembered that if we go ahead with the rescale, prokaryotes will be a lot smaller anyways so having proteins occupy space is a pretty natural way of limiting how many a prokaryote could have. I think the ATP cost though would be the biggest limiting factor, and prokaryotes have a tough time producing large amounts of ATP so it’s a soft cap on how many proteins they could sustain in their cell.

I was thinking more that it would extend the “reach” of your cell when it swims through a cloud, because you’d be able to more quickly absorb the compounds and even absorb ones that are a little farther away, almost like there’s a small magnet on one end of your cell. However I don’t think we should add a “mouth region” part because any segment of fluid membrane should be able do absorbing.

Pretty much what I was thinking. In Microbe you’d place organelles into your cell. In early Multicellular you’d place cells of different customized types, and/or you’d place organelles in one cell and it’d replicate across all other cells of its type. Then in late Multicellular you’d have different tissues available based on what cell types you created in early Multicellular (You could still evolve the other tissue types though). So for example in the Microbe Stage you’d place a vacuole into your cell for storage, in early Multicellular you’d create a cell type called “Fat Cell” and put a huge vacuole in it that takes up all the space, and then in late Multicellular you’d place fat tissue on your organism.

I think it depends. Fat granules, the more I think about them, seem like they are already represented by vacuoles and aren’t necessary. Contractile fibers I think are useful in both stages since in Microbe they’d boost ameboid movement, and microvilli would increase absorption/secretion (maybe there’d be an ATP cost to microvilli since it costs energy to hold your membrane in a deformed shape, like stretching an elastic band). I think it’d be best if as many of the organelles in early Multicellular were in Microbe as well, to help Multicellular feel like a natural extension of Microbe.

#9

Sounds like a good amount of support for option A :slight_smile:

I guess with option B the way to handle Prokaryotes would be something like: all cells get 2 protein slots and cells with a nucleus get 4. So that way every cell would have access to proteins and Eukaryotes could have more simultaneously.

One question about option A is how long will it take to do the 3D modelling? I count 11 potential proteins which could be either hexes or slots (Cold, Heat and Acid resistance, Lysosomes, Peroxisomes, Chemoreceptor, Thermoreceptor (potentially other receptors), Pigment and Immune and potentially Adhesion and Signal depending on how agents work). Also are there any ideas on how to make them visually distinct if they are 3D hexes? Maybe colours?

We could have some “gamey” proteins thrown in too, like “5% health boost”, “5% health regen boost”, “5% speed boost” etc, we’d need names for them. How would you feel about those? Are they tacky and gamey or is it quite interesting because you get to mod your cell a bit?

Increasing your absorption radius sounds like a great bonus to have. Drawback maybe that you also get hit by agents in a larger radius?

“microvilli would increase absorption/secretion” What about something like a bonus to compound clouds you swim through, 10% extra from each cloud? But you also get 10% more damage from agents, because you absorb them faster too?

Thinking about what @andross was saying earlier what do you all think about something like: Pilus does melee damage. If you put an agent gland at the base of it then it becomes an injector. If you put a vacuole at the base it becomes a straw and if you put contractile fibers at the base it can become a spear you can fire.

#10

I really don’t think this is necessary. We’ve got plenty of interesting options without having to add things that are simply “game standards”.

Yes Yes Yes! The amount of interesting gameplay here is phenomenal. I’d like to hear from one of the programmers how difficult this would be to implement.

#11

I’d have to agree with Andross on this one, I feel like those don’t really fit in with Thrive’s atmosphere, plus I think many of those stats are already customizable with existing or soon to be added organelles (for example maybe one of the upgrade paths of the Endoplasmic Reticulum is that it heals your cell faster).

Yeah we could try that, though I was thinking to actually increase the throughput of how many compounds your cell can absorb or release in a given second (for example the current cell has to run a few times back and forth through a cloud to absorb all of it). Also that drawback with agents is an amazing idea I hadn’t even thought of, which definitely would be a drawback of such a mutation.

I really like the idea of cross-grading between these. Quick question though, aren’t the injector and straw pilus performing the same function? Is it worth separating them? I think it’d be better to have a single Injector Pilus that can inject or extract agents, compounds, or DNA.

#12

That’s an interesting idea.

If a pilus were multifunctional then you’d need a way of toggling it while playing between different operations.

Also if it’s multifunctional which agent does it inject if you have several agent glands? That needs to be toggled too. If the agent gland is stuck to it then you’d fix that in the editor.

#13

Ah yeah those are good points. I guess the question is do we want to allow the player to have a multipurpose pilus that can switch between these functions, or does it need to be specified in the editor whether it’s a DNA injector, compound injector, or agent injector. I’m open to either. I think if we go with the second approach we should make the MP cost of crossgrading from one type of injector to the other pretty low, to make it easy for organisms to evolve between them/repurpose them.

EDIT: Also, for differentiating between proteins I think if we can use colour, shape, texture, size, clustering/quantity, and Narotiza’s art skills we could make the proteins differentiable so that you could for example swim past some bacteria and recognize that they are photosynthetic and eat them to try and get a chloroplast.

#14

I’m for option A at this early juncture. Having nucleous slots would need a whole new system to be added to the game and creates division between prokaryotes and eukaryotes.

#15

Ok so Nick and I did some editing of the spreadsheet. I tried to include the points people made above. Here is a bunch of questions for discussion.

  1. With a pilus do you prefer:

A: it’s got multiple modes you can switch between at will. It can stab or inject agents or be a straw. You may also need to toggle which agent is being injected.

B: a pilus is just a tube, on it’s own it does melee damage. If you put a vacuole at the base it becomes a straw, if you put an agent gland at the base it becomes an injector (of that agent), if you put contractile fibers at the base it becomes a spear (can thrust for extra damage).

Personally I prefer B but I’m open to options.

  1. Do you know which 3D models we have? Because I have no idea other than the ones in the game now.

  2. Are there any of the organelles whose function you want to talk about / change?

  3. Are there any organelles you would like to add to the list?

  4. We need to sort out the receptor proteins, like what does having chemoreceptor do? Does it mean you can’t see any clouds at all without it? (If so how could you play?) Does it mean you can see clouds that are off the edge of the screen with the edge lighting up? Something else? All ideas welcome.

  5. In situations where you get a bonus in the editor, for example if you use a straw pilus to exchange DNA with a member of your species or if you perform sexual reproduction, how should that bonus be applied? Do you prefer a discount on all MP costs or an increase in the amount of MP you get. Functionally they are the same. You can buy the same with 150MP as you can with a 33% discount.

One issue with discounts is I’m not sure how well it works if an organelle costs 15MP. We can’t take off 10%, for example.

  1. Should any mutations be locked in the editor? So I think people are quite keen that chloroplasts and mitochondria (and maybe a Nitrogen fixing plastid) require engulfing a prokaryote. Is there a bootstrap problem here? How does the first prokaryote get photosynthetic powers?

Is it that photosynthetic proteins are freely available so the prokaryotes can evolve them and then the chloroplast requires engulfing?

Are there others you think should be locked and why?

Personally I’m quite keen to give a Kerbal like experience where the editor is quite an open place and MP is the restriction. However I’m open to other options.

  1. What are people’s feelings about Thermoplasts.

I like that they have been a part of the project for ages and they are pretty alien. However I’m a bit worried they aren’t consistent with chemistry and that’s a core issue of the game. I wouldn’t say I’m an expert and so if anyone wants to make a science based case for or against them I’d be interested in hearing it.

When I google them I get a lot of Thrive stuff back, lol.

#16

I’d like to consider that no model that is in the svn here: https://boostslair.com/svn/thrive_assets/raw_assets/models/ counts as existing. Because this way we won’t lose the original asset files as we have for all of the current models. Also I won’t allow any blend files to be added that include embedded images, they must be linked with a relative path from the assets/textures folder to keep the file sizes reasonable.

So so far we only have the slightly broken flagella model. And maybe the pilus model (I didn’t download it when the link was posted…).

#17

Finally had a chance to go through the list of changes and here are my thoughts:

The list looks great so far. I have a few questions about some of them:

Microvilli: Why does microvilli increase the yield of compound clouds? Why not have it do what it does in real life? (Which is increase the rate of absorption/secretion)
Antifreeze Proteins: I was imagining the environmental adaptation mutations a bit differently, since a cell that only takes half damage in hotter water will still die but only half as fast. Instead of reducing damage it would simply increase the range of that factor which you can tolerate (i.e. be immune in).
Heat Resistant Proteins / Pigment Protein: Same as above.
Lysosomes: I don’t think it’s necessary to reduce the reproduction cost to represent the digestion performed by lysosomes, since the digestion of lysosomes would already directly represented by them netting you more compounds harvested out of large chunky food.

On the topic of receptors and the receptor mutations, I feel like that’s a good question and I’m not too sure on any answers to it yet. I’ll think about it and get back to you guys once I have any thoughts on it (also it might be worth discussing that one on the protein reception thread).

The idea behind this is that 100 mutation points represents 100% of the possible evolution in a generation.

That’s a very good question. Prokaryotes should be able to evolve the proteins themselves, and eukaryotes should be able to endocytize the prokaryotes to turn them into organelles (called endosymbionts) like mitochondria and chloroplasts. Then the question becomes, could eukaryotes evolve the proteins themselves? Do we want to allow that option? I’m unsure on this so I’m interested to hear what you guys think. Andross suggested that eukaryotes be able to evolve either proteins or endosymbionts. Endosymbionts would be a lot more efficient, but can only be obtained through successfully assimilating a prokaryote.

Another question this touches on is, should all mutations other than endosymbionts be available to the player from the beginning? The original concept for this was no, but I think we should rediscuss this. For example should a player be able to place an Adhesion Protein the first time they enter the editor? If some mutations will start locked how will they be unlocked?

One idea if we have mutation unlocking is that you could start the player with a random selection of mutations unlocked. Players can then unlock new mutations by engulfing other cells (5% chance to unlock a mutation they have), engulf free floating particles of DNA (20% chance), or exchanging DNA with other cells using Horizontal Gene Transfer (Plasmids, Sexual Reproduction, DNA Injector Pilus).

I think that we should keep them as an idea but not worry about adding them yet. I’m not sure what chemicals a thermoplast would use or how it would work. Technically a thermoplast is not even meant to be used on a site of high heat intensity but actually on a site of a big heat gradient, which by its nature will be very temporary.

#18

@NickTheNick Thanks for the input. I agree with a lot of what you’re saying about unlocking.

I’ve got some questions.

When you say Microvilli increase the rate of absorption/secretion what do you mean? At the moment absorption and secretion are instant, if your compound store overflows your cell can dump as much as it likes in one step. So how could we increase it?

With lysosomes can I ask what “large chunky food” is? We have free floating organelles and I am thinking we’re replacing those with prokaryotes. When you engulf the target cell loses health and then when it dies it drops it’s compounds and you pick those up as your reward. So what is “large chunky food”? At the moment the only thing to eat is compound clouds.

I get the idea that 100MP = 100%. How do you give a discount on say Motility CIlia which are slated to cost 33MP. If you take 10% off then they cost 29.7MP, if you take 50% off they cost 16.5MP, are you ok with fractions of an MP? Do you think that’s better than letting people have a bonus of doing 110% mutation this turn?

With antifreeze proteins say I am in a tropical biome with water of 20-30 degrees and I want to move to an arctic biome with water of 0-10 degrees. How do I do that under your system? Because if I don’t have anti-freeze proteins surely I die instantly every time I spawn in the arctic biome? So do I have to add antifreeze proteins while in the tropical biome in preperation? Can I be adapted to both tropical and arctic?

I think in the sunlight thread I was imagining that any cell can go to the tidepool and survive there, it’s just hard. And if you then add pigments it becomes easier to live there. Same with bio-luminescence, any cell can live in a cave but it’s hard until you have a lantern. Do you see what I mean?

#19

Here is an oversimplification of my rant on slack from a few days ago:
I’m all for renaming respiratory proteins to Mesosomes , I’m totally okay with changing name of photosynthetic protiens to Clorophyll, what do you guys thin of that? (they will be the same as they would have been if called them proteins functionally, its just name changes can make it look more sciency and let us drop some helpful info on the real life counterpart in the description. and to appease the peopel complaining about them being called protiens) I know its an oversimplification to do a name change like that and keep the functionality, but im hoping we improve bacteria much more in 0.4.1. (there is an issue on github for it already)

We don’t want to simulate individual ribosomes that’s silly so packaging things together and calling them suchsuch protien is a good way of folding(bacteria pun) these things into a peaceable object but changing a name is alright in my book, until we want to do deeper simulation.

Im also thinking, if we add chemoplasts (and we will as they are planned for 0.4.0) we add a bacterial equivalent in protein form for those aswell to keep things consistent and so bacteria dont just pop immediately like bubbles when they come on screen because they arent surviving heh.

#20

Those all sound fine with me.