Membranes characteristics


#10

I‘m not sure if this kind of reposting is appreciated, but I just found some great concept art of this in another thread (Prokaryote Gameplay)


I thought it might be helpful to put this here. What‘s the point of good concept art if it‘s not visible where people discuss the exact things that concept art explains?
Sadly I don‘t know who created this.

I think this general idea, coupled with a slider, provides the best option. It‘s still a two way slider, but the balancing is more interesting than a simple defence vs speed slider. This way it‘s more defence vs speed vs engulfing.


As you can see in the table above, this could be quiet balanced if we do it correctly.


#11

I‘ve done a finished concept of how the membrane section of the editor would look.

The only slider which the player can control directly is „rigidity“, the other characteristics would change depending on rigidity.
The GUI design is based on @Narotiza‘s Circular health/ATP/reproduction progress bars. During an editor session the player can access the patch map and a report of what happened during the editor session represents.


#12

I like a lot the sliders and how they looks, i have just a question,
what did you image is flagella efficiency?

I imaged a slider of speed that can be increased by adding flagella, reducing by adding other organelles or improve rigidity.


#13

I think cell walls are either very heavy or completely unable to support external organelles like flagella and cilia, and low-rigidity cells are too fluid and flagella would just end up pushing one part while the rest stays behind:


Meaning medium-rigidity cells have the highest flagella efficiency.


#14

But efficiency doesn’t affect speed directly?


#15

@Dak28 Alright, in that case efficiency isn‘t the right word. I meant exactly what @Narotiza was talking about. Is effectiveness the right word?
The idea is that it would be about 100% for microbes with cell walls or normal membranes, but rapidly decrease as cells get more amoeba-like. For microbes with cell walls weight would drastically increase, making autolocomotion increasingly infeasable. But these need to be two seperate stats weight also influences how well a cell can be pushed around, while flagella effectiveness doesn‘t do that.


#17

Hi, bellow you will find a general description of cell membranes and walls. I tried to limit the details to things useful for the game development and put forward some game-related characteristics and ideas. If I went too deep or neglected some details do not hesitate to ask questions and I will be happy to answer.

  1. Membrane(s)

1.1 Membrane fluidity

Membranes may appear as a solid barrier isolating the organelles from the outside world but this limit is actually quite flexible and can almost be considered a fluid. This fluidity is necessary for the cell as it allows the membrane to flex and create vacuoles for phagocytosis. The fluidity of a membrane is strongly influenced by its composition and is usually adapted to the cell’s environment.

Temperature is the main factor when it comes to cell membrane fluidity or stiffness. As a rule of thumb the higher the temperature, the more fluid a membrane becomes, up to the point where it breaks from thermal stress. The opposite is also true and a membrane becomes stiffer the colder it is, eventually impeding the cell’s ability to exchange nutrients and metabolic trashes with its environment. It can become so cold that ice crystals may form inside a cell and, much like a knife, breach the membrane.

In this regard micro and macro organism have a specially tailored membrane composition. Organisms with stiffer cell membranes are usually living in hotter conditions and those with a more fluid membrane tend to be living in colder climates. This, overall means that they have a comparable membrane fluidity but at wildly different temperatures.

The best examples would be extremophiles: thermophile bacteria were found to have “cheated” the usual composition and added special lipids to their membranes that stiffen it a lot, allowing it to tolerate the extreme temperatures found near black smokers. Its membrane would probably be solid at room temperature. On the other end of the spectrum there is an arctic fish that live in waters that can reach -4 degrees Celsius and, yet, does not freeze. It membranes are very fluid and would likely easily break if brought near a black smoker but given the low temperature, it is just fine. It even evolved a natural antifreeze agent that clumps with tiny ice crystals forming in its blood and cells and stops them from growing to a dangerous size.

1.2 Membranes

Some organisms have more than a single membrane. Bacteria have what could be called a triple-membrane as it is composed of an inner lipid bilayer, an intermediate layer of peptidoglycans and another external lipid bilayer. All these layers serve as additional protection and serve as an anchor point for some external structures like flagella.

I do not know much about organisms with multiple membranes however and this is pretty much it from the top of my mind.

  1. Cell walls

2.1 Without cell wall

Most organisms without a cell wall are either amoeba-like or have an internal cytoskeleton made from protein fibers to keep their shape. The greatest disadvantage of a “naked” membrane is osmoregulation as the entirety of the membrane is exposed to the environment. They are, however, those that can engulf the biggest preys and can achieve some motility using pseudopods.

2.2 Cellulose wall

Most common in plants, trees and algae cellulose walls are extremely resilient to internal pressure. If its osmoregulation fails and it would normally burst, the cellulose wall will keep the cell intact for quite some time (I once ran an experiment where we put some carrot cells in distilled water and it took it about 10 minutes before I saw some cells burst). It is also very resilient to physical damage and, to a certain extent, chemical damage. However the right enzyme can make short work of cellulose, take the fungi decomposing wood as an example.

2.3 Chitin wall

Found in fungi, chitin is kind of a middle ground. It does offer some mechanical resilience, it is kind of hard to break down without the right enzymes but is otherwise unremarkable as far as I know. It is very much not my area of expertise though and I am probably missing some details.

2.4 Silica shell

Not a true wall per say but could be considered like it in game mechanics. It allows for some of the sturdiest protection while not stopping light for photosynthesis. A large amount of organisms with a silica shell have spikes and other defensive structures. Ironically most of the organisms with a silica shell move like amoeba, using pseudopods protruding from tiny holes and openings in the shell. The main disadvantage of a silica shell is sheer weight and they have a hard time not sinking. Another disadvantage is the raw material needed to produce this shell and silica can sometimes be a limiting nutrient during blooms. Art note: though most micro-organisms aren’t incredibly cute or something, Diatoms, Silicoflagellates and radiolaria could be called artists and are quite pretty.

2.5 Calcium carbonate shell

There are two types of calcium carbonate shells, those made out of calcite and those made out of aragonite. I do not know if this is too much detail but I will go ahead anyway. Both are quite sturdy and also heavy but most organisms with such shells also have flagella that allows them not to sink or control said sinking. Calcite is most resilient to chemical stress and can stand lower pH than aragonite. Aragonite is, on the other hand, more resilient to physical stress than calcite and relatively sturdier overall. Both have a huge advantage and a corresponding disadvantage. The advantage is that calcium carbonate is extremely plentiful and is almost never a limiting factor to their growth. The disadvantage is that there is a limited depth at which calcium carbonate starts dissolving. At a depth between 4000 to 5000 meters, calcium carbonate dissolves completely and no organisms with a calcium carbonate shell can survive bellow said depth.

  1. Graph

Here is a little graph to summarize it all and a few of my ideas on how it could be implemented in the game.

Membrane/Wall Advantages Disadvantages Example Organisms
Simple Membrane None, standard None, standard Euglena, Amoeba
Double Membrane Chemical and physical resilience Maintenance costs, slower exchange with environment Most if not all bacteria
Without Wall Easy phagocytosis (larger engulf radii), mobility through pseudopods High osmoregulation cost, vulnerable to physical and chemical damage Amoeba, most animal cells, choanoflagellates
Cellulose Wall Low osmoregulation cost, highly resilient to chemical and physical damage Very weak to specific enzymes, low mobility, slower exchange with environment Plants, algae
Chitin Wall More resilient to most damage Lower mobility, slower exchange with environment Fungi, Yeasts
Silica Shell Most resilient to physical and chemical damage, lower cost of spiky defenses, very pretty Very heavy, increases sinking rate dramatically / lowest mobility, increases cost of mobility-related organelles Silicoflagellates, radiolarian, diatoms
Calcium Carbonate Shell Resilient to most physical damage and slightly resilient to chemical damage Heavy, slightly increased rate of sinking / low mobility, slower exchange with environment Dinoflagellates, Coccolitophores

Don’t hesitate to ask questions!


#18

Thanks for all the details and the handy list, this will really help us out. And i agree on most of them. Though im not sure how we make the silica shell work, as “sinking” isnt something we have to worry about in-game right now. Maybe it makes you move slower instead?


#19

In real life it is usually sinking bellow the photic zone that kills diatoms over being eaten but that’s just real life, it is not so fun isn’t it. It would indeed be easier to simply have silica being the “tank mode” and have it move the slowest of them all instead of including a whole mechanic for the rate of sinking.


#20

This is really useful and interesting, thanks for posting this!
Some things I’m curious about:

You mentioned membrane fluidity having to be based around an environment’s temperature for a cell to survive there. Is there a way for an organism to achieve a wider range of temperatures it can survive in? What should the highest range be?

How do you think all this could work with the membrane rigidity slider concept posted above? Do you think a different system could work better? I get the feeling it’d be strange if you were to evolve a silica shell from one of a completely different material, and I believe both a one-dimensional slider and a list of options wouldn’t be very good in that regard.

Could the player mix and match the different membrane and wall types in the editor, or does it make not enough of a difference to matter like you mentioned in the discord?

In the entry for Silica Shells, you said it allowed for “some of the sturdiest protection while not stopping light for photosynthesis.” Are there stronger shells that do block out all the light? I think a wall like that could lead to some interesting gameplay.


#21

This is really great info, thanks for taking the time to write it. I guess the factors that can relatively easily be changed gameplay wise, as you say, are: resistance to physical and chemical damage, movement speed, osmoregulation cost, ability to engulf, amount of damage taken when osmoregulation fails, cost of pilus, depth at which you can exist.

We could maybe change the rate at which you pick up compounds from clouds, or maybe the radius you pick things up from, though that might be frustrating.

In terms of sinking we could have a mechanic like “in order to exist in the mid or high ocean you must be neutrally buoyant or better” with vacuoles and cytoplasm giving buoyancy and having a shell taking it away. That might be interesting. It would also allow the most shelled creatures to exist in the tidepool as they could be as heavy as they want.

I really like that the membrane rigidity can be used to regulate temperature, we haven’t talked too much about temperature but rolling it in to membranes sounds cool.

One question I have is how we differentiate Cellulose Wall from Chitin Wall, they don’t seem to be particularly different. Is Chitin transparent? Maybe that could be a differentiating factor like the shells.

Also, you’re right, radiolarians look great :slight_smile:


#22

Thanks for the feedback,

Regarding the questions:
@Narotiza, In the real world most organisms can survive in a relatively wide range of temperature. The more adapted to extremes however, the narrower the range your membrane will be effective. A middle-range membrane would be you jack-of-all-trades, not better than a specialized membrane in a specific environment and nowhere near able to survive extremes but able to exist in a wider range of temperatures and sharper variations like in tidepools.

Regarding the slider, i agree that this is a very good system and could definitely be used to change the membrane fluidity. Keeping it in the middle would make you great at resisting temperature variations and live in a normal range of temperature but anything a bit more extreme requires you to adapt by changing fluidity.

About the mix and match of membranes and walls, in real life you cannot mix and match any and all and there are metabolic/didn’t-stick-in-evolution reasons, but from a game stand point why the hell not? After all if the player is willing to deal with the consequences of having both a specialty membrane and a wall, this can make for some interesting options. The only limit I see, and that is from a balance/simplicity standpoint, would be to allow only one wall type at a time while any membrane could be combined with it. But again, that is only my way of seeing it and i do not know how hard or easy it is to put in game.

Finally for the Silica shell, I did say it does not block light and I understand that it can be a little misleading. Actually any wall or thicker membrane would block some amount of light. This is not much however, plants do most of the photosynthesis and have cellulose walls. At this scale I am not sure if this actually matters all that much but from a gameplay standpoint it could indeed be a good factor to have walls block some amount of light for photosynthesizing organisms. This amount should be small however as most of the photosynthesizing organisms in real life actually have a cellulose wall or silica/calcium carbonate shell.

@tjwhale, For the rate of sinking, i like the way you brought it up and can tell you some organisms do have vacuoles to increase their buoyancy. Most of the organisms living in the middle or higher part of the ocean rely on currents to keep them in suspension since things do not behave all the same at this scale. Indeed many diatoms, pretty much all those you can see that are oblong oval-shaped or banana-shaped are actually bottom dwellers in shallower waters where they photosynthesize and glue themselves to sand. This glue also holds sand particles together and diatoms are good at control erosion at a micro-scale.

About rigidity, it does not control temperature per say, but rather allows a cell to continue it’s normal life in different temperatures. Like i said earlier to Narotiza, average membranes are the jack-of-all-trade of ambient temperature while more rigid will allow to keep a normal fluidity in hotter environment instead of bursting. Fluidity increases with temperature and resistance is affected by membrane composition. A very rigid membrane will be as fluid in near a black smoker as a very fluid membrane will be in arctic conditions, each being adapted to match its living conditions. However the more specialized you are the least adaptable to change you become.

I must admit that as of right now I am a bit puzzled as to how to differentiate chitin from cellulose. At this scale pretty much everything is transparent to a certain degree but, yes, chitin more-so than cellulose. There are three main differences i can think of from the top of my head but i will look into it today: Chitin is a nitrogen rich-er material than cellulose. Cellulose walled cells tend to be more organised and geometric than chitin-walled cells, plant vs fungi. And last but not least in later stages on the game, cellulose could be reinforced with lignin to allow for woody plants instead of small herbs and ferns.

Hope that helps, do not hesitate to ask further questions!
In the meantime i have an appointment with some reference books to find more information.


#23

I remembered a relatively important thing i forgot before. Cellulose is actually glucose chains that are bound differently from reserve glucose and chitin is nitrogen-enriched glucose that is also not bound like reserve glucose. Figured this could mean additional amonia and glucose to multiply / kind of a small upkeep of both for chitin. Also, an additional glucose cost to reproduce or upkeep for cellulose-walled cells, which, in real life, must allocate carbon to reserves, reproduction and cell wall and maintain some form of balance depending on conditions.


#24

Here’s this silly thing:


I wanted to avoid completely different wall types being direct, linear upgrades of each other, so I made a mockup of a system where, when dragging the rigidity slider, you can pay a certain (relatively large) MP cost to jump a dotted line and unlock a certain wall type. It makes them all unique and unrelated, but I’m worried it also complicates things too much?


#25

@Narotiza I love your doodles of these cells, they look very fun:) But I think your worries are very much warranted…
My counter-proposition: We leave the slider linear. On one extreme there‘s a fluid membrane, on the other extreme there‘s a cellulose/chitin cell wall. We don‘t really know what the gameplay distinction between cellulose and chitin would be anyways, so I propose we just make them the same thing and call it „cell wall“.
As @Estredar layed out in his long post, sicilia and calcium carbonate layers aren‘t really membranes, but shells outside of the membrane. So I propose we just put them into the „external structures“ in the organelle section and make them completely seperate from the membrane rigidity slider.
Something Estredar said which also supports this proposition is that the sicila-shell-bearers have a very fluid, amoeba-like membrane underneath the shell.


#26

Interesting ideas. I agree that having a single slider doesn’t work so well with shells. If we put shells in the external organelles section then they are binary, there is only one thickness rather than a slider.

I’m open to options on this.

One possibility is to have a 2D selector, with the rigidity on the x axis (from soft -> normal -> double -> cell wall (both chitin and cellulose together)) and then have shells on the y axis (silica at the top -> none -> calcium carbonate at the bottom). That way you can have any kind of membrane and then put any thickness of shell around it. Cell wall + thick shell would be the ultimate defensive strategy.


#27

@tjwhale I like the direction you‘re going in. But rather than have a 2D selection we could, you know, have two sliders. That‘s basically the same as far as I understand, just not as confusing to the player.
A reservation I have with either of these options (2D selection and two sliders) is that a slider/dimension which goes from silicia shell to no shell to carbonate shell doesn‘t really have a strong intuitive logic to it. It isn‘t intuitive that no shell is in the middle of sicila shell and c-carbonate shell.
Also a slider/dimension for shells wouldn‘t be able to control where to possible holes and spikes would be located on that shell.


#28

I want chitin cell walls, if we have a slide my proposal is you just choose the “chitin” texture, or the “cellulose” texture so you have some options.

Also, chitin allows for budding, which could be an alternative means of reproduction, so that could be the difference.


#29

THANKS @Untrustedlife, That was the one detail i was trying to remember, budding, yeasts! Yes, chitin wall has the advantage of allowing budding. Budding could be exactly the same thing as mitosis in game with simply a different animation.


#30

Once the rigidity slider enters “wall” territory, allowing the player to choose between different, purely cosmetic textures, based on the different wall types estredar mentioned, is a pretty simple way of doing things, however it doesn’t really show the player how different walls behave if they’re just reskins of the same general wall. It could work if we don’t want to implement different properties yet though, and it could be a nice way for players to customize their cell.

I do want to see different wall types in the game, I’m looking forward to trying to texture the silica shell especially.
(also I still think the chitin texture looks too dark)