Organelles / Mutations

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.

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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.

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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.

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.

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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.

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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.

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…).

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.

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@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?

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.

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Those all sound fine with me.

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tjwhale suggested a nitrogen fixing plastid, it would generate about 0.5 ammonia a second
Do we do it?

Lately I have been thinking about ways we could implement thermosynthesis while making it a unique and interesting method of gameplay.
As you might assume, thermosynthesis seems to be slightly similar to photosynthesis in concept and function. The nature of this relation is most obviously reflected in how thermotrophs in Thrive will more than likely produce scaling amounts of energy based on the ambient temperature of the inhabited patch. I do not want thermoplasts to strictly be a chloroplast that uses heat however, and so the rudamentary proposed stats below will reflect these desires.

Thermoplast:
75C --> 20 ATP, or 0.8 glucose
This is a rather simple exchange, where the cell produces a small amount of energy at optimal temperature. My idea here is that the further your cell is away from this temperature, the less efficient the organelle becomes. Too little heat means not enough energy to work with, too much and it overwhelms and denatures the necessary proteins. Note that these provided numbers are not final, they are intended as a starting point that we can work with to find the optimal values.

I am rather conflicted about what kind of product should be produced by this part. My first choice was ATP as it would create a dynamically different playstyle than photosynthesis, but I fear that it might be unsuitable since unlike iron you wont have any means of storing the energy at all. On the other hand; Glucose is an excellent choice as it will allow the player to survive in cooler areas thanks to their ability to store the excess energy. Glucose would likely require more than just heat to produces however. My only complaint here, and it is rather silly, is that it makes thermosynthesis much too similar to photosynthesis. My instinct is to attempt to make each playstyle as varied as possible, but I shouldn’t let that get in the way so ultimately I will leave this choice to the theorists to decide. I dont believe it is determined what exact products would arise from this process, but I feel they aught to have the final say.

Thermosynthase(?):
75C --> 8 ATP or 0.02 glucose
From what little literature I found in my brief skimming online, a few referenced that thermosynthesis could have potentially been one of the earliest methods of sustenance for early cells. From that I can deduce that prokaryotes would potentially be able to utilize heat much in the same way as eukaryotes, and so I am proposing this prokaryotic variant as a result.
Not much else to say about it really, other that I am rather poor at naming things.

A common idea that has been brought up alongside thermoplasts has been the concept of “hotspots”. Localized zones of higher temperature that could prove suitable for thermosynthesis.
The long standing problem with these however is the difficulty of properly visualizing heat.
My proposal here is that we create models for hydrothermal vents that emerge from the background of the map. These spires would serve as a billowing visual indicator for heated regions, acting as both a hazard, and an energy source depending on your adaptations. These vents would naturally be found in decent quantity within the vents patch, but I believe allowing them to spawn (albeit less often) within the seafloor and abyssopelagic biomes as well would provide for suitable variety. Each vent would radiate a gradient increase in temperature that rises the closer you get to the center, where it would likely be too dangerous for anything to survive. I’m not sure how realistic it would be for there to be vents so tiny, but I feel it would make for an appealing and viable visual.

I would like to hear what others would like to add to these concepts!

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This sounds really nice. I think there is an issue that if thermoplasts work everywhere then there’s no incentive to use anything else.

In terms of “go near a thing to get energy” there’s this radiotrophy concept we worked on for a while. Not sure if it’s the right thing but it’s there if it’s at all useful to you.

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My intention was for the thermoplasts to only really work best in sufficiently heated biomes. That is, in the vents you would passively get some (very meager) energy no matter where you are because of the high ambient temperature, but in other biomes you would have to solely rely on finding small vents to get your energy, as otherwise the overall temp is too low. These environmental vents would only appear in a couple other patches on the sea floor as well, and not too often.

Ah I had forgotten about radiotrophy, thank you for reminding me! I’m afraid it hasn’t sparked any new ideas for thermosynthesis in me, but I do have ideas on how the two organelles can be differentiated in gameplay. I suppose I know what I am going to be looking into next!

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Did you see the point that was brought up last time thermoplasts were discussed, that they physically should work only in a temperature gradient. Based on that the idea was floated around that the player microbe needs to be between hot and cold water for it to efficiently do something. Related to that a basic implementation was suggested: the thermoplast efficiency is determined based on the temperature difference between the current patch and a nearby cooler patch.

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Oh my I must have missed that while scouring the forums for posts about the thermoplast, that certainly complicates things! I suppose I’ll have to step back and rethink this for now, as I dont know much about the details on how that mechanic would work.
Do you know where this point was made? I didn’t see anything on the forums so I assume it was in discord.

It must have been on discord as I can’t find anything related to that on the forums (just that higher temperature is better for thermoplast and that LAWK needs to be off).

Edit: it was confirmed to me that it was on discord.

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Alright so I am back at it again with thermosynthesis, and have a new idea on how it could work.


Basically, the thermoplast will include it’s own “compound bar”. This bar represents the player’s current temperature gradient (I dont actually know anything about temperature gradients) which they have to fill to as close to the indicator line as they can to obtain optimal energy generation. The scaling for this will work similar to photosynthesis in that the bar represents 100%, and the further away from it you are the less you get.
Being in locations under 75C will not fill this bar and will instead slowly drain it, while locations above 75C will slowly fill the bar. As a result, the player must seek out both hot and cold waters whenever needed in order to maintain their gradient and produce energy.
I would like to know what everyone thinks of this!

Edit: To continue with this, the rate of losing/gaining heat in your gradient will be relatively steady and slow (Something like a 0.01 increase/decrease), hopefully so that balancing the gradient is not a tedious act of traveling back and forward between temperatures. I also went ahead and settled with thermoplasts producing glucose as that seems more likely.
Thermoplast:
0.09 CO2 & 1 gradient = 0.12 Glucose
Thermosynthase:
0.09 CO2 & 1 gradient = 0.04 Glucose
Note that the 1 here means 100% which is the value tied to the position of the indicator line. Being below the line means you have less than 100%, going past the line will inverse the increase and again reduce the percentage of glucose you produce.

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Simply placing this updated proposal here so it does not get lost in our developer chatroom.

Bracket is based on a percentage of gradient storage.
First bracket at 30% mark. Second bracket at 60% mark.
Goal of the player is to possess a gradient level confined within this bracket. Too much or too little will result in no ATP production.

The brackets will shift in position based on the player’s local temperature. Residing in a temperature lower than the patch’s median will push the brackets higher, while higher temperatures will push the brackets down.

Since the gradient is mechanically a compound, it shares it’s storage value with everything else. Larger cells have more storage, so they will need more thermosynthesizing parts to maintain their gradient within the brackets which are based on percentage.

Gradient production and consumption will need to be carefully balanced to ensure a general lack of frustration. This will need to be done experimentally.