Epithelial-mesenchymal transition, adhesive proteins and extracellular matrix

[50gens]

@Swampuss

cells with fewer adhesive molecules (and therefore less adhesion) migrate out of cells with more of them

@Swampuss

If we make a slider that is responsible for the strength of adhesion (AM expression level), then even a small discrepancy will cause cell types to line up according to this very strength

How could we design anything at all by saying which cell migrates away from which cell? How does that result in them lining up in a line?

@Swampuss

the fact that specific cells would not be attached to specific points

Colonies do have a fixed number of cells

Eutely

For example, each eye of the tardigrade consist of just one cell*. If that cell moved, it would be like our eyes moving in our bodies, I don’t think that happens.

Obviously, we don’t have a fixed number of cells. This change can happen when the player starts to place tissues instead of cells, the number and position of cells no longer being important.

@Swampuss

it should also be with organelles - they are not located in real cells at specific points and can move through the cytoplasm (except perhaps organelles attached to the cytoskeleton)

I think changing the position of the organelle should be free in the editor, and maybe their positions can change randomly during the gameplay, especially for the cells that move by making pseudopods.

@Swampuss

making it possible to move away from earthly life, for example, by creating four embryonic foliage

This was mentioned in another thread

@BurgeonBlas

4 layers is rather easy to conceptualize: You just have an extra cell line grow out of the ectoderm as well as the endoderm. Or even you could have 2 line branch from the endoderm, or even 2 from the ectoderm

@Swampuss

Well, yes, I’m talking about the fact that in this way it would be possible to build the same germ layers, from which organs are then obtained, while this would be much more convenient and would give much more freedom to the players than if these sheets were written in code in advance.

One could say that placing metaballs for individual cells* is the option with the most freedom.

There isn’t even a need to make germ layers, the player can place cells like a 3d snowflake, but the design can be nudged towards the “lawk” design by the enviroment. The need for diffusion prevents a sphere with an inside that is filled, and the fact that other colonies that can trim (eat) the cells that are too “on their own” would discourage regenerating a snowflake shape. If the cells line up in a plane, they all can do diffusion, but the ends of the plane can still be eaten by larger colonies. A sphere (blastula) is like a plane, but it has no ends, the only way to engulf any cells of it is coming with a larger sphere, or breaking it apart.

Also a sphere is aerodynamic (hydrodynamic?), it shouldn’t have anything around it other than limbs to swim with. To increase the number of cells while maintaining a spherical shape on the outside, folds can be created (epithelial-mesenchymal transition of gastrula), which is like a sphere inside a sphere, but everything is connected.

If we end up having the same degree of freedom as we have now, there can still be a tree diagram of cells specialising from each other, but the order of specialisation wouldn’t need to be correlated with where they are located in the colony (like the endoderm and ectoderm of gastrula)

If we decide that spherical colonies and folds are what always happens anyway, we can instead have an editor that is like spore, you have a sphere and you can click and pull it to make folds. I support taking away freedoms in favour of conveniency, but I was told* that people do like freedom.

@Swampuss

It can be said that my idea is aimed at making it possible to move away from earthly life

If I understood your idea, I didn’t like all of it. You said

@Swampuss

I proposed a relatively convenient way to set up tissues so that you don’t have to manually set all the tissues, well, that is, by setting up adhesive molecules, you could determine what is inside and what is outside

Imagine we will build a lego house. To draw a blueprint, we would draw how it would look, right? We wouldn’t draw the lego pieces, as they are scattered on the ground right now, and draw their free body diagrams with forces that would throw them to the air the right way so that their trajectories would make them land at the correct positions to make a lego castle.

The extracellular matrix and the molecules that pull the cells, are harder to engage with for the player than the final product. Removing the middle step (cell movement) turns EMT from a process the player directs (by changing the densities) into a physics simulaton where the program does everything automatically to reach the end goal or maybe even into a visual problem that the physics engine occationaly gives a thumbs up. Automation will already happen when the tissue editor is added.

@Swampuss

because if they move relative to each other themselves, and not according to the patterns specified in the code, this will bind the players’ hands much less

A spore fold editor could be easy to handle by the player

Spesifying patterns in the code (visual problem version) would things simpler. That is not to say it is unscientific, a “proper” simulation can be done beforehand, and the data from that can be used, if it generalises to any type of fold, and why wouldn’t it, because there is just one variable that pulls the cells, and that is the densities.

@Swampuss

Also, by setting the same adhesion parameters for two cell types, you can make a mixed tissue, since the cell types will be grouped together

Yes, but grouping them together doesn’t help if you can’t even move one of them to a spesific place.

@Swampuss

Imagine, for example, a sausage, it has an intestine in the center

That was quite an amusing thing to imagine. But I get what you mean. There is an animal with a digestion system, which marks the front-back axis.

@Swampuss

A similar thing happens between the eye bladder and the ectoderm of the head during the formation of the eye of vertebrates , this is called induction

Cells differentiating based on where they are in the body. Does this make a difference for the multicellular editors?

@Swampuss

when the muscles interact with the ectoderm, it would turn into ligaments

Would this be true for an alien? What does ectoderm mean anyway?

@Swampuss

In fact, in order to create a limb, one would have to do something akin to a notochord (or simply draw out an exoskeleton), after which both muscles and ectoderm will automatically appear that would control this limb

I think this is a good idea for muscles. For example, for a hinge joint, a flexor and an extensor can be placed at the right locations by the editor.

But, think about octopuses, they neither have bones, nor and exoskeleton, yet they have limbs. And not all bones in our bodies make limbs. I think we should just place a blob that is a limb, it gets muscles, but it gets bones later, or optionally.

@Swampuss

Instead of manually making all the muscles and building a limb, one could simply gradually stretch it, in fact, this is how limbs are built at the embryonic level - first it is baking the ectoderm, then the mesoderm enters there, after which the limb continues to stretch and form it skeleton and muscles

I imagined streatching a part in spore creature editor. That would be easier than carrying twenty metaballs.

@Swampuss

I would say that it would be cool to have a larger variety of enzymes that could possibly interact with each other and lead to denaturation of each other, so that life does not seem like honey, and you can’t just take and learn how to digest everything at once. By the way, one could find out why different enzymes are secreted in different glands in order to understand this better

Interesting. But I though an enzyme had only one substrate, which isn’t something as large as another enzyme.

I don’t know why an enzyme would denature another. Maybe it can change the enviroment (like ph) and make it unsuitable for the other one, but that is an indirect way. But normally, they should be able to work together, and not interact.

@Swampuss

As if many things were done not according to a specific program given to them, but according to a general program according to which everything else works, as far as possible

Do you mean newton’s laws of motion? As far as possible isn’t as far as simulating atoms, that’s for sure

@Swampuss

It doesn’t exactly repeat evolutionary history.

@Swampuss

It seems to me that the best way to make a game is to make it simulate life on a fundamental level, the level that everything else comes from.

@Swampuss

As for me, the best option is to simply make a number of fundamental algorithms and actions for each stage, on the basis of which all the others are built, and then cover all this with convenient controls. Thus, we will get a game with a very high freedom for the player, convenient control.

That’s the hope. The thing is, conveniency may be hard to achieve, but you can always ignore the details, and put a cutscene from the end of tribal stage and start in industrial scene, like spore did. That’s not what I suggest, what I say is that I wasn’t able to imagine how I would change the density in the extra cellular matrix and make the cells move into a blastula shape. Even if I could, I wouldn’t want to do it, especially for every step in the embriogenesis until tissue editor becomes a thing. Taking the evolutionary history is a shortcut, and not entirely unscientific.

@Swampuss

the mutation of the HOX gene does not just move the limb, it moves the entire segment on which it is located

oh okay

@Swampuss

this is the same as with insects - in order to fly, you must first grow flat processes on your back, then enlarge these same processes, attach muscles to them, etc., in order to eventually learn how to fly.

Exactly. In spore, you would place a wing, and you could suddenly fly, for a short time. And by doing so, you would turn your creature into a hexapod if it was an tetrapod, even though repurposing an existing limb has to take less time and dna ponts that creating a new limb from scratch. Segment duplication doesn’t tend to happen in vertebrates

If we don’t have a momentum for what we are building, if we dont have to stick to our creations and find ways of morphing into new purposes, than stuff like this

@Swampuss

many arthropods have fewer limb-bearing segments than vertebrates, as evidenced by the number of nerves that we have per limb (we seem to have five of them each, while arthropods have only one), and we can say that each of our limbs is a combination of several others

wouldnt matter. It is just a leg, being the product of a merger or starting out with the number we have now doesn’t make a difference. But the philosophy of spore, and thrive, is designing everything around you in the game, the past decisions effecting the future. Well, maybe not so much in the case of convergent evolution, but still.