Microbial Compounds and Organelles

Ah, thermoplasts. Alright, so chloroplasts use light for photosynthesis. Thermoplasts use heat for photosynthesis; the idea is that heat emits infrared radiation, which is an electromagnetic wave. So light. It's much less effective to use that part of the electromagnetic spectrum, so it's only useful if it's the ONLY part of the electromagnetic spectrum available. If you've ever heard of "Black Smokers" (hydrothermal vents deep, deep down in the sea) this is pretty much the only place where thermoplasts can be considered to exist. They don't use chlorophyll because..well..why would they? So they're not chloroplasts. Also to my understanding Carbon is replaced by Sulfur in this photosynthetic reaction.

Binary fission is the division of an entire organism into two halves which later regenerate. That means if you have a single cell there's little you can see to differenciate it from mitosis, but once you're talking about metazoans the difference is obvious. A good example of that would be platyhelminthes. So binary fission in procaryotes is mitosis, and it's more complicated than mitosis when it's binary fission for a metazoan.

Gluers. I'm not sure what you mean by that, especially the bit about DNA. As I'm French I assumed in my language the term was just very different from "gluers" but it appears to rather be a word meant to explain the function than the scientific term since on the first page I saw an article about women who glued a man's penis to his abdomen because he was unfaithful. So I will assume you mean the extracellular matrix which keeps different cells together. If it is the extracellular matrix I may have some things to say about that.

You do not need centrioles for cell mitosis. Plants simply don't have them. I'm not too knowledgeable on the subject, but a bit of research could give us something to go.

Respiration is incredibly convoluted if you assume the point is just to get a proton on the other side. But that's not the point. But it's not. The point is to be as long a circuit (for the electron) as possible so that you benefit fully from this free (powered by gradients) source of energy. It would be more convoluted to have a different circuit for each step and evolution doesn't like waste. So again, it's good that it's circuitous because that's more efficient.

Cell walls at a unicellular stage mean that, for gameplay, you'll either need to eventually lose them to reach a (fun) metazoan gameplay, or you'll stay stuck as a microbe/become a plant. A mushroom if you're lucky. Furthermore you mention the importance of silicate but that's pretty much just diatoms. If you're an alga it's mostly about sugars, proteins come into play when the cell is done growing but that's of little importance. Or, you know, have Belgium science. Which is really funny to me as a Frenchman because we often joke about the Belgian as though they were lesser people. Kind of like Americans and Canadians.

You mentioned membranes that act as filters, and suggested it could depend on the size of the nutrients going in, that's entirely true: if your membrane is permeable enough to allow a fatty acid to just waltz through your cell must be torn open. However there is an exception: membranes are not permeable to ions, you need specialized ion pumps. (Water has its own pumps too. Just anything that's charged doesn't get through because a membrane is a lipid bilayer and thus has a hydrophobic core which doesn't allow charged molecules through).

When a mitochondria/chloroplast is assimilated to your cell, you might want to call it endosymbiosis just to be more precise.

Cilia are much smaller (about 10x) than flagella, and they have a second basal body (which you really, really don't need to bother caring about).

ATP gives energy when it's broken into ADP+P, and it takes very little energy to attach that P back to make it ATP again. Actually this is what ultimately happens with respiration, an electron goes around oxydating and all the while activates pumps which expulse protons many steps of the way, which causes chimio-osmosis and the protons comes back through an ATP synthetase.

Finally this last comment is just for my curiosity:
Clone Stickers. I've been unable to find any mention of them on Wikipedia and they seem really interesting.

The extrace- The gluers come in three different types:
Animal gluers are collagen, it's made out of proteins.
Fungi gluers are chitin, a glucose polymer which happens to be what arthropod exoskeletons are made out of.
Plant gluers are cellulose, incredibly tight glucose associations. You need to be a fungi or specialized bacteria to be able to assimilate it.

Binary fission is a mode of asexual reproduction. If you're a unicellular organism it means a single mitosis. If you're a flat worm it means cutting yourself in half and then regenerating each half with multiple mitosis. It only exists because when a worm does that you can't say "Oh that phenomenon is called mitosis" because it doesn't refer to a single cell. The concepts are similar, but not the same.

Well, first off there are two types of flagella, there is the prokaryote flagella which essentially houses a rotor which can operate at 6,000 to 17,000 rpm (thank you Wikipedia) and is so complex and efficient that creationists are trying to use it as an argument for intelligent design. It functions like a propeller and the filament (which is not surrounded by the cell membrane) can reach 200 to 1000 rpm, apparently allowing all the way up to 60 cell lengths / second
Then there's the eukaryote flagella, surrounded by the membrane, which beats in a sinusoidal fashion if used to get around. If it's used as a sensory organelle it's for all intents and purposes a tentacle. I suggest keeping the two possibilities separate to avoid convoluted controls ("Hold Alt+Shift to enter sensory tentacle mode! Left click is for the left tentacle, right click for the right tentacle!").
Finally, cilia, those are about 10 times smaller than eukaryote flagella, and that's all the difference you'll notice. They don't quite beat in the same way, but no one will care if you use the exact same sprite or whatever as long as it's smaller.

I can't find any studies as to the different speeds and efficiencies of cilia and flagella, but a fair compromise would procaryote flagella = 10 eucaryote flagella = 10 cilia. With efficiency being procaryote>cilia>flagella. The drawback of being a procaryote is..well..you're a procaryote. You can't get past microbial stage, and we can say that 10 cilia are more energy efficient than one flagella, but take up more space on your membrane which you might want for endocytosis or a silicate cell wall. Or just to look more aesthetic. A final point on flagella, the procaryotic ones are not made of the same proteins as the eucaryotic ones/cilia. Also a procaryote can't get cilia.

Code:

ejectedMass=mps*time
mass -= ejectedMass
speed += ((0.5*ejectedMass*(soe)**2)*2/mass)**(0.5)
speed -= 9.8*time

Where:
mass -> Mass (in Kg) mps -> Ejected mass per second (in Kg/s)
time -> time since last iteration (in seconds) soe -> speed of fuel being propelled backwards relative to the rocket (in m/s)
The other are self-explanatory

The double * means raising to the power of wathever is on the right

As you can see, all that formulas get much simpler on a computer.