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 Microbial Compounds and Organelles

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NickTheNick
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PostSubject: Microbial Compounds and Organelles   Sat Nov 10, 2012 3:18 pm

On this thread we will brainstorm and discuss the different compounds and organelles that are necessary for the Microbe Stage. We need to identify the significant properties of these compounds and organelles, and how they relate to the player and the organisms. The processes between these compounds will have more detail in their own thread, as will the weightings of the processes. Lastly, we need to also include attachments to a cell like cilia, flagellum, ionic pumps, etc.

-------------------------------------

Organelle List

Orange numbers are now organelles that can be gained through mutation and not through endocytosis. Their new names and any new notes on them are given here.
1)flagellum- can evolve from cilia or vice versa
2)cilia- can evolve from flagellum or vice versa
3)lamellipodes- these are rigid exoskeletal extensions that act like legs
4)pseudopodic movement- this will be available to a player whenever their cell membrane is loose enough around the central cytoskeleton to allow it, and will not involve a specific visible organelle, but will require a mutation giving it the ability to coordinate large membrane movements.
6)Conjugal Nuclei- extra nuclei within the cell used for sexual reproduction; if you reproduce sexually, your population can grow more rapidly and you can evolve more rapidly as well. There will probably be many ways to sexually reproduce, and asexual reproduction is an option as well.
7)Predatory Pilus- the description there seems great to me
8 )Slime Gland- vacuole that fills with antiphagocytic slime and can be released upon contact with another cell.
16)Cell Wall- can be added to outside of membrane and attached to cytoskeleton. This protects you from the elements and other cells to a certain extent, depending on its thickness. However, it does restrict your motile and feeding abilities somewhat, which we can detail at some later point.
17)Communal Membrane Proteins- these are membrane proteins that can evolve that allow you to attach to other members of your species.

Green numbers can be achieved through mutation or engulfment.
5)Bioluminescence can be achieved through the assimilation of luminescent bacteria, or by the development of a luminescent organelle.

Blue numbers can be gained exclusively through endocytosis.
11)Mitochondria begin as free-living aerobically respirating bacteria engulfing them has a 1 in 1000 chance of symbiosis, which will dramatically increase the efficiency of your cell. It will be virtually impossible to survive without gaining them fairly early in the game.
12)Chloroplasts begin as free-living sessile cyanobacteria. Engulfing them has a 1 in 2000 chance of symbiosis. They will need mitochondria to function, and can only function, and are only found, in well-lit environments. They won't
be around in the initial ocean vent biome.
13)Thermoplasts will be found as free living sessile bacteria in the initial biome. They have a 1 in 2000 chance of becoming symbiotic. They will only work in very hot areas, but can work without mitochondria, albeit not very efficiently.

Any numbers not listed above will either be standard organelles (vacuoles, lysosomes) or not included (producers, dissolvers)

Many of the organelles will have several different stages of efficiency, such as the lysosomes, mitochondria, chloroplasts, and thermoplasts. This list is not final: it is an attempt to make cell stage organelles sensible and scientific. Please add your thoughts.

-------------------------------------

I will make a working list of all the compounds and organelles as we think of them, along with their properties, below.

Compounds

Amino Acids
Ammonia
ATP
Carbon Dioxide
Ethanol
Fatty Acids
Sugar
Heat
Lactic Acid
Light
Methane
Nitrogen
Oxygen
Protein
Water

Organelles

Organelle --- Process: Reactants = Products - Catalysts

Chloroplasts --- Photosynthesis: 6 Carbon Dioxide + 6 Water = 6 Oxygen + 1 Glucose - Light
Mitochondrion --- Aerobic Respiration: 1 Sugar + 6 Oxygen = 6 Water + 6 Carbon Dioxide + 38 ATP - No catalysts

Instincts

Energy
Nourishment
Growth Progress

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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 5:41 pm

I have two organelles: chloroplasts and thermoplasts. In-game they create glucose and oxygen from water and carbon dioxide at a rate proportional to the amount of light or heat in the area. 6 units of carbon dioxide and 6 units of water are needed to make 6 units of oxygen and 1 unit of glucose.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 5:43 pm

So how would heat and/or light factor into that?

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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 5:50 pm

The greater the heat/light, the greater the rate of reaction. So 100% heat/light (on whichever the scale the game uses is) might have the reaction applied say once per second, whilst 0% heat/light has no reaction. 50% light/heat would be 0.5 Hz, and so on.

EDIT: You forgot to put oxygen onto the compound list, that will be important once someone gets round to making mitochondria.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 7:34 pm

So I wasn't able to find anything on thermoplasts. What are they and how do they work? (I'm assuming they are a thermal counterpart to chloroplasts.)

Also, what organelles are necessary chemosynthesis?

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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 8:16 pm

As far as I'm aware, neither thermoplasts nor chemoplasts actually exist in nature (life as we know it). However, both are sufficiently feasible and interesting for us to include in Thrive, and will presumably work in a similair way to chloroplasts. Chemosynthesis does occur in nature, but (to my knowledge) only in protokaryotic cells, so there is no organelle for it. Someone will have to do some research on how exactly it works, but again adding a 'chemoplast' is fairly reasonable.

Also, to save you guys starting from the very beginning, I recommend reading the compound system thread, which already contains a sizable list of compound and their interactions, summarised by this chart:



The chart also gives some process names, though no weightings. The second page of that thread also explains how reaction rates will be calculated, based on the concentration of input and output compounds, and an intrinsic rate. That intrinisic rate is all we need for each reaction, and it should be a simple number, not an equation. For example, if (I'm making these number up, at some point they need to be researched) aerobic respiration happens twice as fast as photosynthesis, aerobic respiration may have an intrinsic rate of 1 reaction per millisecond, and photosynthesis 0.5 reactions per millisecond. (actually, reading above, Hz is a good unit for this).

The above chart covers most of the basic compounds (though there may be more). Note that heat and light are not compounds, but they are handled that way for the moment. What we really need is more advanced compounds, e.g.:
- phospholipid, creating from ~20 fatty acids + 1 triglyceride (~= 0.5 glucose), used in the creation and repair of cell membrane. Can also be broken down into the above for energy.
- protein pump, created from proteins/amino acids, used to deliver compounds across the cell membrane.
- cellulose, created from monosaccharides (~= glucose), used for creation/repair of cell wall.
- cell surface receptors, created from protein and monosaccharides, used for cell-cell adhesion and recognition.
- enzymes, created from proteins/amino acids, used for just about everything a cell does...

It would also be good to have an estimate of what goes into building an organelle (i.e.: 1000's or 10'000's of protein, phospholipid, 100's cell surface receptors, pumps etc.)

Hope this all helps. I'll try to contribute to this when I can, but I'm already occupied by several other things I really should be working on instead.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 8:18 pm

I'll see what I can come up with for chemo or thermosynthesis.

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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 8:26 pm

Seregon, is it fine if we call monsaccharides sugar? Just for simplicity's sake.

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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 8:29 pm

For simplicity, yes, and as far as the game is concerned there probably won't be a difference (differentiating monosaccharides would be too much detail). Just remeber that sugar (i.e.: glucose) is one example of a monosaccharide. So whenever you talk about sugar, glucose, or monosaccharides, your talking about the same thing (as far as Thrive is concerned).
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PostSubject: Re: Microbial Compounds and Organelles   Sat Nov 10, 2012 8:34 pm

Gotcha. I also included methane since when I was reading about chemosynthesis it said that methane was one of the commonly consumed chemicals in the process.

@sciocont: Thanks for the help. I think having photo, chemo, and thermo diversifies the paths available to both the player and the CPU for evolution.

EDIT: For new organelle submissions, use the aforementioned format below.

Organelle --- Process: Reactants = Products - Catalysts

A quick Biochemistry 101:
Organelle means the name of the organelle, pretty self-explanatory.
Process is like the ability that the organelle unlocks. Since this is a game, it should be helpful to think of them as that. For chloroplasts, the process is photosynthesis.
Reactants are the compounds that go into the process.
Products are the compounds that are produced by the process.
Catalysts are any factors that increase the rate of reaction, based off of Hz. For example, the reaction rate of photosynthesis is based off of the concentration of light, with 100% light resulting in 100% reaction rate.
Remember to include the weightings of the products and reactants if possible.

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PostSubject: Re: Microbial Compounds and Organelles   Mon Nov 12, 2012 3:24 pm

I realize this is already in the code, but it's nice to add it to the comprehensive list.

Mitochondrion --- Aerobic Respiration: 1 Sugar + 6 Oxygen = 6 Water + 6 Carbon Dioxide + 38 ATP - No catalysts


(Are there any catalysts to Aerobic Respiration?)

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PostSubject: Re: Microbial Compounds and Organelles   Tue Nov 13, 2012 3:48 pm

NickTheNick wrote:
I realize this is already in the code, but it's nice to add it to the comprehensive list.

Mitochondrion --- Aerobic Respiration: 1 Sugar + 6 Oxygen = 6 Water + 6 Carbon Dioxide + 38 ATP - No catalysts


(Are there any catalysts to Aerobic Respiration?)
I've recently had a biology lesson on this subject - the mitochondria do in fact contain catalysts for aerobic respiration!

But what they are exactly, we were not told, and apparently neither was Wikipedia… That's worrying.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Nov 13, 2012 4:10 pm

Do you mean catalysts, or enzymes? As far as I'm aware only enzymes are involved in most biological reactions, whereas catalysts are ussually used in industrial processes.

If your after the enzymes involved, this pdf gives a very detailed explanation of respiration and the enzymes involved. Probably far more detailed than we need though.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Nov 13, 2012 4:38 pm

Seregon wrote:
Do you mean catalysts, or enzymes? As far as I'm aware only enzymes are involved in most biological reactions, whereas catalysts are ussually used in industrial processes.

If your after the enzymes involved, this pdf gives a very detailed explanation of respiration and the enzymes involved. Probably far more detailed than we need though.
The enzymes act to catalyze the reaction, though they are not typical catalysts like metal surfaces. They are protein enzymes so we needn't make exceptions or extra rules regarding them.

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PostSubject: Re: Microbial Compounds and Organelles   Tue Nov 13, 2012 7:20 pm

I apologize, maybe my use of the word catalyst wasn't entirely appropriate. What I meant by catalyst was it's literary sense, such as an impetus or stimulant, just any factors that would speed up the reaction.

EDIT: Also, I remember in a past thread roadkillguy explicitly stated that he was thinking of only coding in about 6-7 compounds. In the list I have above we already 14. Should we worry about complexity, or is this fine?

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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 15, 2012 12:32 pm

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.
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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 15, 2012 7:30 pm

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.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Dec 16, 2012 8:09 pm

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?

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PostSubject: Re: Microbial Compounds and Organelles   Mon Dec 17, 2012 12:19 pm

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.


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PostSubject: Re: Microbial Compounds and Organelles   Mon Dec 17, 2012 3:55 pm

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 ?
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PostSubject: Re: Microbial Compounds and Organelles   Tue Dec 18, 2012 11:58 am

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.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Dec 18, 2012 9:39 pm

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.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Dec 18, 2012 10:27 pm

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.
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PostSubject: Re: Microbial Compounds and Organelles   Wed Dec 19, 2012 12:33 pm

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!
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PostSubject: Re: Microbial Compounds and Organelles   Wed Dec 19, 2012 6:31 pm

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.
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PostSubject: Re: Microbial Compounds and Organelles   Today at 4:02 pm

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Microbial Compounds and Organelles
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