Microbe -> Multicellular transition

I'm not 100% familiar with the planned future features of Thrive, but here's my two cents (although this doesn't address the issue of how the game would recognize when a certain cell qualifies as a certain tissue type).

I think each stage's editor should retain the editor of the previous stage. So in Multicellular you would still use the cell editor to upgrade cells and create new ones, and now you would also have the tissue editor to arrange cells to create tissues. In Aware stage you would no longer have access to individual cells, but you would still use the tissue editor to upgrade tissues and create new ones, and the "parts" editor becomes available. In Awakening you get the parts and tools/techology editors (or something along those lines), and so on.

So anyway, in Multicellular stage you'd start with a colony of your cell from the Microbe stage and whatever cell you've binded to.
The cell editor gets a few new features:

• A list of all your cell designs (only one or two at the start). Select one in the list to spend MP in the same way as before.
• A list of all the tissue types as described earlier in this thread. This will give you the information on what is required to create the tissues recognized by the game.
• Create a new cell design, starting from one of your existing ones.

And now the player has access to the tissue/organism editor where they can organise groups of cells in more or less the same way as organelles in the cell editor (but 3D).
I'm not sure if your creature is supposed to have actual parts like legs, organs, etc. at this point. If so, this new layer of the editor should also have a list of parts which you can edit and use to design your organism.

Basically each cell has it´s own special proteins, for example muscle has myoglobin, a protein that gives it it´s red color among other things, nerve cell has a special outer layer that allows it to conduct electricity, it would not be able to do so otherwise, other cells have similar specialized structures that allow them to function in the capacity then need, also there are certain rules governing this, muscles that needs to move things (as opposed to muscle that is just there to fix things in place) always comes in pairs, you have a biceps and a triceps, one contracts when the other stretches and vice versa, you can´t get a functional limb otherwise, nerves consist of two parts, dendrite and neurite, dendrite receives the message from the last nerve cell and passes it on to neurite that is a lot longer and moves the message along, in practice dendrites serve as pit stops for messages while neurites are the actual fiber that transmits the message over large distances. So how can you simulate this, well maybe adding myoglobin to cell walls makes it able to stretch and contract better, this could be introduced in the late cell stage as an upgrade for cells that move with pseudopods, and just continued from there, as i understand it first stage of multicellular organism is a bacterial colony, in a small colony bacteria should be able to communicate just fine by pheromones, but as the colony grows larger there is increasing delay, so making a long cell with the ability to receive a signal on one end and emit it on the other end (using specialized structures you could unlock) could be the first stage of a nervous system, as you improve this cell it could emit messages over larger and larger distances. Hope this helps.