Microbial Compounds and Organelles

For organisation, I'll quote the Seregon's answer here.

Seregon wrote:

The issue of having too many compounds has been raised and discussed in the compound system thread. As I explained there, we're not coding in any compounds. Rather, we build a system in code which reads compounds in from files. That way, we can very simply change the detail of the system without touching the code.

The plan was to start with a relatively accurate and details system, test it, and then simplify as needed.

One reason for this is that the more compounds we have, the more mutational options species have. Having just 5 or so compounds (probably air, water, energy, nutrients, and possibly protein), would severely limit the complexity, and probably diversity, of the game.

Yeah thanks for the reply. That edit was from before I posted on the Miscellaneous Bugs and Suggestions Thread, but no one was answering it.

So could you guys post organelles for the Microbe Stage here and I will compile them in a word document. If there is already a list somewhere please link it to me.

Also, for the organelles you post, can you please include the processes they enable/undergo or any significant details about them that the game needs to know? Thanks.

EDIT: Oh yeah scio, what did you come up with for chemo and thermo synthesis?

I assume they will need a way to be gained, too, so I'll make a list based on our current proto-cells. I'm not quite sure what you mean by ‘significant details’, so I'll just write anything that comes to mind.

Based on our current proto-cells:

n) Proto-cell - Organelle - Processes - Significant details

1) Wrigglers - Flagellum - Propulsion, often sensory* - A tail-like means of propulsion.

2) Writhers - Cilia - Propulsion/sensory* - Hair-like, and similar to the flagellum in structure, cilia have many uses in multi-cellular creatures. They come in motile and non-motile varieties*.

3) Squirmers - Lamellipodium - Relatively rapid propulsion* - A cytoskeletal protein actin projection on the mobile edge of the cell*. Fun fact: I had never heard of such a thing before now.

4) Squishers - I don't think this technically counts as an organelle - Amoeba-like movement - Movement in a squirmy way.

5) Shiners - Bioluminescent dot - Bioluminescence - A dot which shines when the cell feeds. Probably best for top predators.

6) Clone-Stickers - Pilus - Cloning - Stabbed into another cell, to inject ‘reproductive material’ into another, causing them to die and be replaced by a clone of the former species. Have a very complicated page on Wikipedia.

7) Poison-stickers - Pilus - Poison - Stabbed into another cell, to inject a toxic material into another, causing them to die and dissolve into an edible material.

8 ) Defenders - Antiphagocytic capsule - Resistance to phagocytosis (absorbtion) - ‘Produces an outer coating of enzyme "slime"’

9) Producers - ? - +Nourishment - From proto-cells description: ‘Transform the amino acids into proteins. …grants the player double nourishment from absorbing Amino Acids, and allows damaged cell components to be replaced.’

10) Dissolvers - ? - +Nourishment - Again, from proto-cells description: ‘Reduce [proteins] to amino acids. …grants the player double nourishment from absorbing Protein, and allows cells with Walls to be consumed.’

11) Eaters - Mitochondria - (Cellular) Respiration (It's complicated) - Small dots. Allows the consumption of carbohydrates (glucose) for energy, but also take part in many other cell functions*. Have their own DNA*.

12) Light-eaters - Chloroplasts - Photosynthesis (6CO₂ + 6H₂O + Energy (Light) → C₆H₁₂O₆ + 6O₂) - Small green dots. Transform light into carbohydrates (glucose).

13) Heat-eaters - Thermoplasts? - Thermosynthesis - Don't ask me to explain how this works. If you want to know the equations, you can try asking in The m=c Thread. (I told you it would be a success! )

14) Cookers - Lysosomes - +Nourishment - ‘Release enzymes which break down proteins and cells into amino acids’. Do various other things*.

15) Holders - Vacuoles - Storage -
From Wikipedia, since it already has a list of stuff, which is all fairly important:
Isolating materials that might be harmful or a threat to the cell
Containing waste products
Containing water in plant cells
Maintaining internal hydrostatic pressure or turgor within the cell
Maintaining an acidic internal pH
Containing small molecules
Exporting unwanted substances from the cell
Allows plants to support structures such as leaves and flowers due to the pressure of the central vacuole
In seeds, stored proteins needed for germination are kept in 'protein bodies', which are modified vacuoles.

16) Platers - Cell walls - Defence - Form a protective barrier around the cell. ‘In silicone-rich environments, these may be 1.5x as hard to puncture/engulf (as they utilize silicate crystals)’. Rigidity varies*. I suppose I should also mention it is a layer on the exterior of the cell, just beyond the membrane.

17) Gluers - More to do with the DNA than organelles - Multicellularness - Allow a cell to bond with others of its type, or glue (sic) them together.

*According to the great book of knowledge, Wikipedia.
Otherwise, either my knowledge or from the description of the proto-cell.

The Uteen wrote:

11) Eaters - Mitochondria - (Cellular) Respiration (6O₂+ 6H₂O → C₆H₁₂O₆ + 6CO₂) - Small dots. Allows the consumption of carbohydrates (glucose) for energy, but also take part in many other cell functions*. Have their own DNA*.

I'm quite sire this formula is wrong. you have 12 C on the right side, and none on the left side. wouldnt it be 6O2 + C6H12O6 ->6H2O + 6CO2 ?

Daniferrito wrote:

The Uteen wrote:

11) Eaters - Mitochondria - (Cellular) Respiration (6O₂+ 6H₂O → C₆H₁₂O₆ + 6CO₂) - Small dots. Allows the consumption of carbohydrates (glucose) for energy, but also take part in many other cell functions*. Have their own DNA*.

I'm quite sire this formula is wrong. you have 12 C on the right side, and none on the left side. wouldnt it be 6O2 + C6H12O6 ->6H2O + 6CO2 ?

I really need to stop making stupid mistakes like that. I even had the actual formula open. Fixed.

I'll add energy into the equations, too, since they aren't much use without it.

Yes, adding energy into the formula makes more sense. However, i'm not sure about this formula:

6O₂ + C₆H₁₂O₆ → 6CO₂ + 6H₂O + Energy (ATP)

Acording to what i saw, ATP is C₁₀H₁₆N₅O₁₃P₃. So now we are missing all those components from the left side. However, i only have a basic grasp on chemistry (enough to know some formulation), and even less biology or biochemistry. Furthemore, all the formulas on wikipedia seem to lack some components when synthesizing ATP, usually phosfor, so i might just be missing something.

ATP isn't directly part of the reaction, rather the energy released by the above reaction (respiration) is captured and used to convert ADP -> ATP (adenosine di-phosphate -> adenosine tri-phosphate) in a seperate reaction. Similairly, when ATP is used to provide energy in some other part of the cell, it is converted back to ADP.

In fact, respiration is actually a series of about 10 different reactions with multiple intermediate compounds, summarised as C6H12O6 + 6O2 -> 6CO2 + 6H2O, which is simply the overall reaction.

Keeping all that in mind, all the game needs to know is that ATP is produced as a bi-product of respiration (we don't need to track ADP, or the extra phosphate), at a rate of roughly 36-38 ATP produced per 1 glucose.

Daniferrito wrote:

Yes, adding energy into the formula makes more sense. However, i'm not sure about this formula:

6O₂ + C₆H₁₂O₆ → 6CO₂ + 6H₂O + Energy (ATP)

Acording to what i saw, ATP is C₁₀H₁₆N₅O₁₃P₃. So now we are missing all those components from the left side. However, i only have a basic grasp on chemistry (enough to know some formulation), and even less biology or biochemistry. Furthemore, all the formulas on wikipedia seem to lack some components when synthesizing ATP, usually phosfor, so i might just be missing something.

Well, that's the last time I refer to Simple Wikipedia.

P.S. Ooh, there's a tag for _subscript text!

Just to make sure, is this interpretation of The Uteen's list accurate?:

1-4 Propulsion. Intake ATP to move the cell. (Generates some toxins as byproduct?).

5 Light. Would it run off ATP or just as byproduct? I mean, does it have a negative impact?

6 Reproduction

7 Easier to eat. Probably 6 and 7 cost some resources (proteins?) to be used.

8 & 16 Defense. What difference apart from the resources it cost? can be had both at the sime time? Do they restrict propulsion (namely squishers)?

9-14 Transformers. Transforms compounds into another compounds (byproducts, extra resources needed?) Also you mention Walls in 10, but it isn't in the list.

15 Storage for certain compounds, like toxins generates as byproducts, or things that the cell can't hold normally

17 Just enables for multicelular.

- Nucleus Althrough it isn't listed here. Maybe because it doesent transform compounds. It still plays an important role (unlocking organelles?)

Apart from all the stuff they intake/produce, we also need a cost of producing the organelles.

If we want our cells to be able to undergo mtiosis, we need centrioles.[i]

In which way does mitosis differ from just binary fission?

For example, deuterosome and protosome differenciate in that the first opening in the 8 cell "sphere" becomes either the anus or the mouth. But for what we care, that doesen't make any difference.

Daniferrito wrote:

In which way does mitosis differ from just binary fission?

For example, deuterosome and protosome differenciate in that the first opening in the 8 cell "sphere" becomes either the anus or the mouth. But for what we care, that doesen't make any difference.

binary fission occurs in prokaryotes, mitosis happens in eukaryotes and is more complex because eukaryotes are more complex.

Seregon wrote:

ATP isn't directly part of the reaction, rather the energy released by the above reaction (respiration) is captured and used to convert ADP -> ATP (adenosine di-phosphate -> adenosine tri-phosphate) in a seperate reaction. Similairly, when ATP is used to provide energy in some other part of the cell, it is converted back to ADP.

In fact, respiration is actually a series of about 10 different reactions with multiple intermediate compounds, summarised as C6H12O6 + 6O2 -> 6CO2 + 6H2O, which is simply the overall reaction.

Keeping all that in mind, all the game needs to know is that ATP is produced as a bi-product of respiration (we don't need to track ADP, or the extra phosphate), at a rate of roughly 36-38 ATP produced per 1 glucose.

Respiration is bullshit chemistry. Seriously, the cell goes through around a dozen steps and many accessory chemicals all to get Belgiuming protons on one side of a membrane. It's the most convoluted thing I've ever studied, but it's worked well enough for however many billion years.

Yes, i saw that part of prokariotes and eukariotes, but bassically, what they are doing is divide. I assume the resoure it takes to divide is just the total cost of remaking every organelle, and maybe the more complex a cell is the longer it takes, but apart from that, what else? Even if the names are different, if they do the same things (in what we care) we can just treat them as equal.

Edit:

~sciocont wrote:

Respiration is bullshit chemistry.

Is the Belgiun filter off, or does it treat you differently?

Daniferrito wrote:

Just to make sure, is this interpretation of The Uteen's list accurate?:

1-4 Propulsion. Intake ATP to move the cell. (Generates some toxins as byproduct?).

5 Light. Would it run off ATP or just as byproduct? I mean, does it have a negative impact?

6 Reproduction

7 Easier to eat. Probably 6 and 7 cost some resources (proteins?) to be used.

8 & 16 Defense. What difference apart from the resources it cost? can be had both at the sime time? Do they restrict propulsion (namely squishers)?

9-14 Transformers. Transforms compounds into another compounds (byproducts, extra resources needed?) Also you mention Walls in 10, but it isn't in the list.

15 Storage for certain compounds, like toxins generates as byproducts, or things that the cell can't hold normally

17 Just enables for multicelular.

- Nucleus Althrough it isn't listed here. Maybe because it doesent transform compounds. It still plays an important role (unlocking organelles?)

Apart from all the stuff they intake/produce, we also need a cost of producing the organelles.

The nucleus isn't unlockable, it is there from the start, so there isn't a proto-cell to unlock it. As far as I know, it doesn't really affect gameplay very much, either, since all in-game cells have a nucleus.

If anyone wants to see the list of proto-cells, it's in the OP of this thread. If your questions aren't answered there, then it is currently undecided. You'll need a biologist to answer most of your questions, my knowledge of organelles really isn't sufficient for this kind of thing, but I do know that cell walls were indeed included - #16.

Then we are starting with eukaryote cells? Everywere i saw a reference to that, everyone said we were starting with prokaryote cells.

Daniferrito wrote:

Then we are starting with eukaryote cells? Everywere i saw a reference to that, everyone said we were starting with prokaryote cells.

Hm… I hadn't noticed that, probably because I didn't know the definitions until now. The advantages/disadvantages of having a nucleus seems pretty important, yet my knowledge of organelles is yet again insufficient. Perhaps I should just stick to discussing space…

Getting back on topic, we need an answer to your previous question.

how would a selectly permeable membrane work in thrive?


(Selectivly permeable membrane is when certain nutrients pass when others such as sugar doesn't)

Just leting some compound through and stoping others? I dont really see what needs to be explained.

In case you are asking about implementation, we could just have a list of what can't go thru and if one tries to pass, just dont let it.

If this filter is based on size of the particles, we can have the particles ordered by size, make the membrane remember its thereshold and dont let pass anything below it.

sounds good to me

next question what about osmosis?

I will let a better qualified individual answer that. I would like to point out on a separate note that this thread is for compiling a list of compounds and organelles for the Microbe stage. Please take minor questions like this to the misc. thread.

actully osmosis is a huge part in the life of a cell

I'm not denying that, I'm saying that discussion here should be geared directly towards compounds and compound processing. More general questions about Microbe Stage need their own thread, or go on the misc. thread.

There is no Belgium filter, we just choose to say so to retain some class. Obviously class was no longer in question in scio's case.

Back on topic, I have two organelles for propulsion. I already knew about these from Spore and basic High School Sciences, but nothing more. Please fill me in on any significant details I am missing about the organelles, or suggest some of your own.

Flagella
Cilia

However, I think it should be possible for the cell to have some basic movement even before acquiring either of these organelles, even if it is not scientifically accurate.

EDIT: Strange, some of the posts before mine just got deleted.