CPA Master List

Theory
1

Trying to make the CPA system prototype without a finalised CPA master list is very difficult. It’s hard to work out if the results are weird because the underlying system has holes in it or because the implementation has problems. Therefore, and because it’s a task we need to do at some point anyway, I think we should make a full and final list of compounds, processes and organelles for the microbe stage. There are previous attempts at this here and here.

Compounds:

Environmental

Sunlight
Sulfur : S
Hydrogen Sulfide : H2S
Oxygen : O2
Nitrogen : N2
Carbon Dioxide : CO2
Ammonia : NH3
Phosphates : PO4

Manufactured by microbes.

ATP : Not specified or conserved. It’s just a currency.
Light - Bioluminescent
Glucose
Pyruvate
Amino Acids
Fat
Protein
Agents
Nucleotide
DNA

Processes:
Chemosynthesis: 6CO2 + 12 Hydrogen Sulfide -> 1 Glucose + 12 Sulfur
Photosynthesis: 6CO2 + Sunlight -> Glucose + 6O2
Glycolysis: 1 Glucose -> 2 Pyruvate + 2 ATP
Respiration: 1 Pyruvate + 3 Oxygen -> 3 CO2 + 18 ATP
Sulfur Respiration: 1 Pyruvate + 3 Sulfur -> 3 CO2 + 3 H2S + 8ATP
Protein Synthesis: 1 Amino Acid + 4 ATP -> 1 protein
Protein Digestion: 1 Protein -> 1 Amino Acid
Amino Acid Synthesis: 1 Pyruvate + 3 ATP + 1 Ammonia -> 1 Amino Acid
Amino Acid Digestion: 1 Amino Acid -> 2 ATP + 1 Pyruvate + 1 Ammonia
Fatty Acid Synthesis: 9 Pyruvate + 56 ATP -> 1 Fatty Acid + 9 CO2
Fatty Acid Digestion: 1 Fatty Acid -> 6 Pyruvate + 45 ATP
Nucleotide Synthesis: 1 Glucose + 1 Phosphate + 8 ATP + 2 Amino Acid -> 1 Nucleic Acid
Nucleotide Digestion: 1 Nucleic Acid -> 1 Glucose + 2 Amino Acid + 1 Phosphate
Agent Synthesis: 1 Protein + 5 ATP -> 1 Agent
Agent Disgestion: 1 Agent -> 1 Amino Acid
DNA Synthesis: 1 Nucleotide + 5 ATP -> 1 DNA
DNA Digestion: 1 DNA -> 1 Nucelotide

Nitrogen Fixation: 1 N2 + 16 ATP -> 2 NH3
Denitrification: 2 NH3 -> N2 + 10 ATP

Here is a chart of the above.

CPAChart3.png982×760 43.9 KB

CPA Organelles:

Chemoplast : Chemosynthesis
Chloroplast : Photosynthesis
Cytoplasm : Glycolysis, Fat Synthesis and Digestion, Amino Acid Synthesis and Digestion
Mitochondria : Respiration
Sulphur-Mitochondria? : Sulphur Respiration
Agent Gland : Agent synthesis
Nucleus/Endoplasmic Reticulum/Golgi Body: Nucleic Acid Synthesis, DNA Synthesis, Protein Synthesis
Lysosomes: Protein Digestion, Nucleic Acid Digestion, DNA Digestion, Agent Digestion

(Therefore the minimal viable cell is Nucles/ER/GB + Cytoplasm)

Utility Organelles:

Flagella
Cilia
Pilus? (Either a hair like appendage or one of these )
Directional Agent Secretor?
Water Pump
Microbial Eye?
Engulfing Edge
Bioluminescent Gland?
Plant Cell Wall
Cytoskeleton?
Vesicle/Vacuole

(Looking through wikipedia’s list of organelles looks like we’ve got a pretty complete list)

2

Agents will have different sizes and compositions, and I think we could make their exact metabolic costs slightly randomized, though bigger agents would diffuse slower and be more likely to be specific or potent (maybe as an agent evolves, the formula to create it slowly changes too, getting bigger/smaller as the agent gets better, etc). For now, we could just throw any simple combination of a few amino acids and maybe a sugar or nucleotide or something.

Copied over from the parent thread:

That’s the logic that led me to produce the list I linked :stuck_out_tongue:. In these equations I made sure to keep carbon balanced, ignored the production and incorporation of water since the amount of water turned over through chemical reactions is always very small compared to the amount of water a cell requires for all sorts of other reasons (ie, a scenario where water is a limiting factor in a reaction is a scenario where the cell has a whole lot of other problems), and used ATP not so much as a chemical compound, but as a unit of energy accounting, to quantify the number of ATP-equivalent units of energy usably produced, or required, by each reaction.

So, for example, you will note that the fat reactions don’t preserve pyruvate, but that’s ok since carbon is preserved, and excluding photosynthesis, ATP is generally lost in reaction cycles, as it should be, since the Gibbs potentials are what drive these reactions in a certain direction in the first place.

How are you driving reaction rates? I imagine you are doing a simple rate law thing. This is a problem with the current game too, since reaction rates in living cells are controlled heavily by gene expression, ligands, etc, and are thus not simply driven by the quantities of each reactant and product. The question is, how do we quantify those regulating factors?

I think what we need to do, just as much as producing a set of processes that doesn’t have any hidden perpetual energy sources, is come up with a specific rule for the rate of each process. For example, what determines the rate at which a cell produces ATP through respiration? Or glycolysis? Or deamination?

3

Yeah I think it’s fine to ignore water if you live in the ocean, makes sense you would never run out of it. However things like oxygen and, as you say, carbon need to be conserved.

I’d rather balance everything. I think it’s just easier in the long run rather than trying to take shortcuts. I don’t mind doing all the work to do the balancing.[quote=“Moopli, post:2, topic:167”]
How are you driving reaction rates? I imagine you are doing a simple rate law thing. This is a problem with the current game too, since reaction rates in living cells are controlled heavily by gene expression, ligands, etc, and are thus not simply driven by the quantities of each reactant and product. The question is, how do we quantify those regulating factors?
[/quote]

Interesting. I was thinking of making a “compounds in a bag” prototype for that reason. We do need to be careful about perpetual motion.

4

We could further tie this into this discussion to finalise other aspects of each compound, such as colours and representative icons, for game builds in the closer future (the CPA system doesn’t need to be implemented wholesale until around 0.5.0, but compound colours and icons will allow compound clouds and the GUI to be updated, for instance).

I made this table in the GDD by collating some of the known compound information and making things up (the icons, for instance, are just guesses right now). Below is a table of organelles, and below that a table of processes. I agree that now is the time to fill those out as much as possible, and confirm all the choices already there.

5

Nice to know we’ve actually had 3 lists :smile: In the end we’ll get down to 1.

6
2 Likes
7

Ok, so for each compound we need to define a few things: chemical composition, colour, symbol, relative weight, additional notes and probably some other stuff. If we can start getting a complete list or table with all of these things decided upon for each compound, that should cover enough for the compound part of the prototype (processes and organelles will still be required though).

8

7 posts were split to a new topic: Compound Colors

9

Ok so some more thoughts:

  • I don’t think we should include water in our reactions – overall, biochemical reactions will generally not appreciably change the amount of water in the system, compared to the amount of water required for biochemistry as a solvent or for myriad other reasons.
  • On that note, trying to balance water will only lead to tears.
  • If we aren’t balancing water, then we really shouldn’t be trying to balance everything at all – we should just make sure that the change in free energy in each reaction makes sense, and that carbon, nitrogen, sulfur, etc (everything except oxygens lost/gained due to water, and hydrogen) are balanced, in most cases. Anything more and we risk creating reactions that don’t make biochemical sense.
  • Hydrogen is another thing that we should not be trying to balance freely. Protons are important parts of a lot of biochemical reactions, yes, but their purpose depends greatly on a bunch of other factors – for example, what they are bound to (or whether they’re simply free), etc. I simply folded the protons involved in catabolism (eg, those bound to NAD+, or FAD+2) into their ATP-equivalent amounts of energy, for example.
  • The exact amount of ATP involved in respiration, and Fatty Acid metabolism is subject to some tweaking – which I think is best done by having a range of possible ATP yields/efficiencies that can get better with evolution up to a certain point.
  • I think, if we’re going to add Sulfur, and Phosphate, that it might make sense to add, say, iron, and nitrate, the first as another source of energy for chemosynthesizers and the second for a better nitrogen cycle. Luckily, as with the sulfur cycle, the CPA system still works even if those are not taken into account.
  • As for sunlight, I’m not sure what the best way to calculate solar energy for photosynthesis would be, but I don’t think it would work to simply have a ‘sunlight’ reactant that scales the photosynthetic reaction. After all, if the CPA system works to maintain certain levels of every compound, then it won’t be easy to keep photosynthesis rate scale properly with sunlight.

Processes:
Photosynthesis: 6CO2 -> Glucose + 6O2
Glycolysis: 1 Glucose -> 2 Pyruvate + 2 ATP
Respiration: 1 Pyruvate + 3 Oxygen -> 3 CO2 + 18 ATP
Protein Synthesis: 1 Amino Acid + 4 ATP -> 1 protein
Protein Digestion: 1 Protein -> 1 Amino Acid
Amino Acid Synthesis: 1 Pyruvate + 3 ATP + 1 Ammonia -> 1 Amino Acid
Amino Acid Digestion: 1 Amino Acid -> 2 ATP + 1 Pyruvate + 1 Ammonia
Fatty Acid Synthesis: 9 Pyruvate + 56 ATP -> 1 Fatty Acid + 9 CO2
Fatty Acid Digestion: 1 Fatty Acid -> 6 Pyruvate + 45 ATP
Nucleic Acid Synthesis: 1 glucose + 8 ATP + 2 Amino Acid -> 1 Nucleotide
Nucleic Acid Digestion: 1 Nucleic Acid -> ???
Sulfur Respiration: 1 Pyruvate + 3 Sulfur -> 3 CO2 + 3 H2S + 8ATP
Nitrogen Fixation: 1 N2 + 16 ATP -> 2 NH3

If we don’t include nitrate:
Denitrification: 2 NH3 -> N2 + 10 ATP (some bacteria convert NH3 to NO3/NO2 aerobically, producing some energy, and others use NO2/NO3 as electron acceptors in anaerobic electron transport chains – adding them up we get about 8-10 ATP being recovered)

In the interest of keeping this discussion moving I’ve forked the colours discussion out so both can continue independently.

10

I have updated the top post significantly. Does anyone have any comments or suggestions? Now would be a great time to speak up if you have opinions on this as I’d like to move towards finalising the list and closing the discussion. I know DNA hasn’t really been on the list before however I think it’s kind of the star of the show. What do the rest of you think about it?

11

I think with DNA these would work better:

  • X NA + X ATP -> 1 DNA (where X only depends on what ratio we want. I prefer X = 1 for the same reasons I prefer 1-1 AA-protein, which I think we’ve discussed before)
  • I don’t think DNA digestion should produce any ATP – the energy in the ATP is used up mainly in synthesis, there isn’t enough left for the reaction to produce ATP and still be able to drive itself forwards.

With those changes, it might be worthwhile to simply rename Nucleic Acids to nucleotides, because it just makes more sense. Last time we decided to remove them, it was cuz we couldn’t justify modelling them independently, but now we can: DNA is built from them, and they can also be used in the production of organelles (them becoming locked would simply symbolize the production of ribosomes, etc, and other uses).

Oh, and for NA synthesis and digestion (or nucleotide if we go ahead with the rename), we should throw a phosphate in there.

As for Agents, I think their digestion should be into Amino Acids, with no ATP recovery, and done in lysosomes.

All in all, I like it.

12

Have made the changes (not to the image though). Will add phosphate if you’re sure it’s worth it.

The reason I had 4 Nucleic Acid -> 1 DNA was because you needed A,C,G and T, thought that was cute. I agree with you 1 -> 1 keeps it very simple.

13

So I looked up bioluminescence, and it turns out that there’s no actual organelle for it. I’m not sure if you guys would want to fit this into the CPA system, but bioluminescence is the result of the oxidation of a compound known as luciferin.

There are many different kinds of luciferin as it has evolved in different species over the course of time. Firefly luciferin requires ATP to use. The chemical formula for FF Luciferin is C11H8N2O3S2.

It’s a bit on the expensive side but it’s the more realistic option. Just gonna leave it here for you folks to decide what to do with this info.

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14

Yeah interesting. I suppose it could be an agent which glows when you emit it. It’s probably easiest to have it be it’s own organelle. Not sure. Maybe it’s nice if it’s an abstract thing you can add to your microbe which makes the whole thing glow. It’s really a graphics decision I think.

I’m really looking forward to deep dark gameplay. I love the idea of swimming around in the dark and not being able to run your lights all the time. I think that’s cool.

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15

Made a mistake. One of the community forumers (early0000) pointed out to me that certain Eukayotic protists actually have a bioluminescent organelle.

It’s not understood how it works though so… I’m also leaving it up to you to decide.

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