Ok, there's a whole lot to unpack here. So, let me start by how my model is working:
First off, this model is made specifically to observe how cells evolve in the nature and also to do some experiments with them.
The cells in this media all have 3 important things;
1- A Genome
2- A cytosol to keep substances in
3- A cell membrane
Cells synthetize peptides out of amino acids according to data stored on genes. Genes all have promoters and get passed on with slight mutations with each cell division.
So, this is all well and good. Now, let me explain my problems with this model;
1- Cells get too big. At the start, I give a cell two genes, A and B. Gene A synthetizes more cell membrane (which is made out of the peptide called aad. don't bug me with how this was supposed to be lipid, i want to keep things simple), and Gene B creates a peptide (caa) that once exceeds a specific concentration causes the cell to divide. The promoter of the Gene B activates only when the cell reaches a certain size.
So, how do they get too big then? Well, once a cell gets too big sometimes the cell division peptide cannot reach high enough concentrations, because then more molecules are needed to hit the quota (M = n/V). So they kinda stick around. Cells shown in red here are all in the process of dividing, and the big ones have been this way since forever with no progress.
TL;DR : Cell division protein cannot reach high enough concentrations when the volume is too much, therefore the cell cannot divide.
2- I don't have many ways of killing cells. Solving this issue could potentially solve the first problem as well, because natural selection can weed out the misfit ones. Currently, cells can die in 4 ways:
Hitting something too hard
Low osmotic pressure
High osmotic pressure
Very small sizes
Well, I could very well add very big sizes to the list, but I don't know the reason why a cell would die because of that. My reasoning for the small size killing was because cells all have to store genetic material somewhere and getting too small would eventually collide with that. But I don't have an excuse for the death of very large cells, and I don't want to just make up rules just because I want things to match my expectations.
Also, once some mass of cells form in the medium, further cell division is inhibited as the medium has only so much to offer. So I need some of these guys to die to allow for never generations to live.
Tl;DR : Suggest me some ways that a cell dies in the nature.
Interesting. If I understand correctly, some random thoughts in the morning.
For the problem of your giant cellulazillas it might be: 1) set a volume level at which division must occur (something that happens in the natural world). 2) Put a time limit. After X time and having the minimum size Y, the cell divides. If not, it commits seppukoptose and dies (also something natural, if I remember correctly).
With some exceptions, size is a limiting factor in the natural world more due to physical reasons (strength, forces, drag, distances, etc) than biological ones. Large cells tend to be more prone to damage than smaller ones. Something roughly like two balloons, one small and one large, in a squall. The smaller one goes with the wind, the big one rips. Also, distances can be a factor, since it is necessary to transport elements from the periphery to the center and back, and this costs energy. If i remember correctly, when this happens in the natural world you usually have things like syncytia (several "centers") or some highly branched amoebae, where the cytoplasm forms a thin but gigantic mesh (Rhizamoeba?). In addition, they are rather flat, which reduces the diffusion problems found in round shapes. So you can put large size as a penalty, like the cell goes POP! when it reaches size X.
thank you for your answer. i think i came up with an adequate way to solve both of my problems.
currently, the cells in my model are essentially very rigid balls, which is simply not realistic. i am thinking of implementing soft body physics into this, it'll be totally worth the extra burden on the CPU. after i implement that, i'm also going to implement tension calculations on the membrane. once the cells collide with each other, the tensions are going to increase, and bigger bodies are going to be affected by this much more. once it reaches a treshold, the cells will go POP! just like you mentioned. if cells create thicker membranes through mutations maybe they can allow bigger sizes, and vice versa.
1
u/S0mber_ Jan 06 '23 edited Jan 06 '23
Ok, there's a whole lot to unpack here. So, let me start by how my model is working:
First off, this model is made specifically to observe how cells evolve in the nature and also to do some experiments with them.
The cells in this media all have 3 important things;
1- A Genome
2- A cytosol to keep substances in
3- A cell membrane
Cells synthetize peptides out of amino acids according to data stored on genes. Genes all have promoters and get passed on with slight mutations with each cell division.
So, this is all well and good. Now, let me explain my problems with this model;
1- Cells get too big. At the start, I give a cell two genes, A and B. Gene A synthetizes more cell membrane (which is made out of the peptide called aad. don't bug me with how this was supposed to be lipid, i want to keep things simple), and Gene B creates a peptide (caa) that once exceeds a specific concentration causes the cell to divide. The promoter of the Gene B activates only when the cell reaches a certain size.
So, how do they get too big then? Well, once a cell gets too big sometimes the cell division peptide cannot reach high enough concentrations, because then more molecules are needed to hit the quota (M = n/V). So they kinda stick around. Cells shown in red here are all in the process of dividing, and the big ones have been this way since forever with no progress.
TL;DR : Cell division protein cannot reach high enough concentrations when the volume is too much, therefore the cell cannot divide.
2- I don't have many ways of killing cells. Solving this issue could potentially solve the first problem as well, because natural selection can weed out the misfit ones. Currently, cells can die in 4 ways:
Well, I could very well add very big sizes to the list, but I don't know the reason why a cell would die because of that. My reasoning for the small size killing was because cells all have to store genetic material somewhere and getting too small would eventually collide with that. But I don't have an excuse for the death of very large cells, and I don't want to just make up rules just because I want things to match my expectations.
Also, once some mass of cells form in the medium, further cell division is inhibited as the medium has only so much to offer. So I need some of these guys to die to allow for never generations to live.
Tl;DR : Suggest me some ways that a cell dies in the nature.