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 Microbial Compounds and Organelles

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Nimbal
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PostSubject: Re: Microbial Compounds and Organelles   Tue Nov 05, 2013 3:40 am

NickTheNick wrote:

I would recommend that the code references from agent be changed to compound
I'm fine with that. It shouldn't be much more than a simple search and replace.

NickTheNick wrote:

Distributing Compounds to Organelles
This could work. The major drawback I see is that this approach leads to organelles working in a "round robin" fashion, with the player having little or no control over the order in which organelles are updated. It also precludes any prioritizing of the organelles.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Nov 05, 2013 11:39 am

Quote :
A furnace can only smelt (process) one unit at a time
You didn't mention the issue of how long a process should take, but i plan on making it flexible, so you can define it per processing organelle.

Quote :
I suggest we just use arbitrary units of measurement
Agreed.

Quote :
Distributing Compounds to Organelles
I see a few potential problems with this:

  • It removes the possibility of priority. Say if you want your life essential systems to get higher priority (aka. getting most or all of the necessary resources), than those producing toxins. Which might not be an issue, tho.
  • Unstable production rate. The player would in some intervals get a quick supply of ATP for example, while the Mitochondrion are at the top of the list, but then when the turn goes to some other process using glucose, the player would notice a period where no ATP is produced even though he may have/be collecting more glucose, it just disappears and doesn't result in more ATP (glucose hungry organelle).
  • What if the organelle at the top of the list isn't done producing yet, from the last time it was on top of the list. Sure you may fill its internal storage for the next round, but then if it still isn't done the next time around, you would either have to wait for it to finish and then give it resources or throw it to the back of the list, giving even less stable production rate.
  • It seems like a very unnatural way for the biological processes to behave.

These problems mostly relate to special cases, but generally it just doesn't seem as flexible as other solutions (like nimbals suggest, or the way it's currently implemeneted which gives compounds to a random candidate which needs it.

Quote :
Feature idea, courtesy of crovea: Vacuoles should have a maximum "bandwidth" for distributing agents to other organelles.
I have two reasons for this, none of which relates to making it a feature for players directly. First supporting argument is that it seems natural that 3000 ATP can't be moved instantly to the organelles that need them, second reason is that it solves a small programming/implementation problem. I also don't see any arguments against it. As of right now it is implemented as a hard cap that says a maximum of 10 units from each compound type can be distributed per second to organelles (1 per 100ms). Changing it to something else like 5 units per second is just changing a number, but it could also be made more flexible (altough i think a hard limit makes sense).


Related question: Excess products from a process that can't be stored by the cell, because it doesn't have appropriate vacuole or they are filled, are just ejected from the microbe right?
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PostSubject: Re: Microbial Compounds and Organelles   Tue Nov 05, 2013 1:00 pm

crovea wrote:

Changing it to something else like 5 units per second is just changing a number, but it could also be made more flexible (altough i think a hard limit makes sense).
I'd like it to be configurable per storage organelle. Mostly because it would open up another upgrade path. Vacuoles could be upgraded to either increase storage capacity or increase their input / output.
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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 07, 2013 2:44 am

crovea wrote:
You didn't mention the issue of how long a process should take, but i plan on making it flexible, so you can define it per processing organelle.
Yes, it's up to the process how long it takes.

Nimbal wrote:
This could work. The major drawback I see is that this approach leads to organelles working in a "round robin" fashion, with the player having little or no control over the order in which organelles are updated. It also precludes any prioritizing of the organelles.
crovea wrote:
These problems mostly relate to special cases, but generally it just doesn't seem as flexible as other solutions (like nimbals suggest, or the way it's currently implemeneted which gives compounds to a random candidate which needs it.
Oh, I didn't realize there was already something in place, that's good then. I agree though with what you said.

crovea wrote:
I have two reasons for this, none of which relates to making it a feature for players directly. First supporting argument is that it seems natural that 3000 ATP can't be moved instantly to the organelles that need them, second reason is that it solves a small programming/implementation problem. I also don't see any arguments against it. As of right now it is implemented as a hard cap that says a maximum of 10 units from each compound type can be distributed per second to organelles (1 per 100ms). Changing it to something else like 5 units per second is just changing a number, but it could also be made more flexible (altough i think a hard limit makes sense).


Oh, so that's what was meant by a "bandwidth" limit. I agree then, that is necessary, because osmosis and diffusion rates (aka "bandwidth") are very real and significant in molecular biology. You don't need to change it to 5. That was just a random example to illustrate my point. However, it's not only vacuoles that have a limit as to how fast they can exchange compounds. The cell itself is limited by this. It can't immediately pick up 500 glucose. It has a rate based on the number of exposed hex faces (surface area) it has.

crovea wrote:
Related question: Excess products from a process that can't be stored by the cell, because it doesn't have appropriate vacuole or they are filled, are just ejected from the microbe right?
I was going to say yes, but then I realized that, due to what we just said above, a cell can't always do that. It might produce 100 units of waste, but have a rate of diffusion of 10 units/second. It would have nowhere to store them, because the vacuoles would be full. All I can think of is that it would burst the cell, but in that case I would imagine cells would burst very often. Do you guys have any solutions to this?

Also, I just want to point out, i think 36 is a more accurate number for the yield of ATP from one process of cellular respiration (it was originally 38). If there are any biologists here please correct me if I'm wrong. I've seen conflicting numbers from different sources but 36 was predominant.

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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 07, 2013 4:21 am

Quote :
It might produce 100 units of waste, but have a rate of diffusion of 10 units/second. It would have nowhere to store them
If you hadn't brought this up, it would have ended up with an implementation where output were transfered instantly. I can see the inconsistency in this, however. We could implement a kind of 'cytoplasm space' where compounds can reside (and even let the cell burst if it gets filled to a limit) and diffuse to and from. This might, however, be overly complex for what we need. Perhaps the simple 'products-move-instantly' approach is good enough.
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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 07, 2013 7:04 pm

How about an organelle only begins a process if there is space to hold all of its products?

If this was the case, products would go into the vacuoles for storage. Then, any products that are needed by the cell (say a process produces glucose which is stored in a vacuole, and there is another organelle in the cell that needs glucose) stay in storage to be used. Any products that aren't needed (say the same process produces CO2, but no organelles need it) then it is expelled.

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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 07, 2013 8:27 pm

Quote :
but no organelles need it
Define need. Do you mean that they can use it at some point because it's part of their "recipy", or that they are currently missing it to start production.

A case: Say some organelle uses water. Then the mitochondria will not produce ATP if the water vacuole is filled? If thats what you're suggesting there are obvious problems with it ;P
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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 07, 2013 8:45 pm

Need as in it is a reactant or required compound for any organelle in the cell. Also, a vacuole would be able to hold any compounds. But that does raise a good point. A plant cell, for example, needs water for their chloroplasts (photosynthesis) but also produces water from their mitochondria. That would mean their vacuoles would eventually just only hold water and there would be no room for anything else. We'll have to do instant expelling of products then until we can get a solution.

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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 07, 2013 8:54 pm

Quote :
Also, a vacuole would be able to hold any compounds
Oh... that will.. require some changes in the implementation then.
I assume it can hold a mix of different compounds in one vacuole then or is it only one type of compound per vacuole but the vacuole can be changed to hold something else.

I'll be heading to bed now tho, brb 11 hours
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PostSubject: Re: Microbial Compounds and Organelles   Thu Nov 07, 2013 10:58 pm

Quote :
Oh... that will.. require some changes in the implementation then.
I assume it can hold a mix of different compounds in one vacuole then or is it only one type of compound per vacuole but the vacuole can be changed to hold something else.
Yeah, vacuoles are just general storage. Otherwise cell's would have to have so many vacuoles just to hold what they need.

crovea wrote:
brb 11 hours
Hah, okay, see you then.

Well, I discussed this with dani, and we got a solution laid out. Any feebback/criticism is welcome. The second idea I came up with myself for a simpler solution.

Solution A:

A vacuole will at all times excrete unnecessary compounds. However, when it is 80% full or more (that threshold is up for revision) a vacuole starts to excrete NECESSARY compounds, no longer undergoes any processes, and no longer intakes any compounds. This means that even if the cell consumes glucose, it will excrete any glucose in the vacuole until it is below the threshold again. However, it always begins by excreting compounds that are in the most excess. Also, the cell only begins to excrete necessary compounds after ALL unnecessary compounds have been emptied out. 

Okay, how does the cell tell whether a necessary compound is in excess or not? Look at the following example.

A cell has 1 mitochondria and 2 chloroplasts in it. The total "demand" or "need" of the cell is:

Mitochondrion #1:
1 Glucose
6 Oxygen

Chloroplast #1:
6 Water
6 Carbon Dioxide
(Sunlight isn't a compound)

Chloroplast #2:
6 Water
6 Carbon Dioxide

Therefore, the total is:
1 Glucose
6 Oxygen
12 Water
12 Carbon Dioxide

This is assuming all of the above organelles process at the speed, let's just say all of them finish a process in 1 second. This is basically the ratio of compounds that the cell needs in order to keep working. When deciding what to expel, the vacuole gets rid of anything that is over this ratio. So if that cell contained 15 glucose, 90 oxygen, 180 water, and 200 carbon dioxide, it would get rid of the carbon dioxide first, because the carbon dioxide is over that ratio and is therefore in excess. If there are multiple compounds in excess, the vacuole randomly excretes between those two.

However, this means that there could be a scenario where a cell is over 80% full but the storage contains the perfect ratio. In this case, one unit of a random compound is expelled. Doing this will break the ratio, which will cause the vacuole to start excreting the excesses again. If the ratio is met again, then another random one will get kicked out, causing there to be excesses and the vacuole ejects them, and this will keep going until the capacity is back under 80%.

Solution B:

A vacuole will at all times excrete unnecessary compounds. However, when it is 80% full or more (that threshold is up for revision) a vacuole starts to excrete NECESSARY compounds. This means that even if the cell consumes glucose, it will excrete any glucose in the vacuole until it is below the threshold again. However, it always begins by excreting compounds that are the lowest priority. All compounds found in the microbe stage have an inherent priority. Also, the cell only begins to excrete necessary compounds after ALL unnecessary compounds have been emptied out. 

For example, say a cell is storing water, oxygen, and glucose. All of these are necessary compounds, and all unnecessary compounds have been emptied out but the vacuole is still over 80% full. The cell will begin to excrete the lowest priority one first. Water has a low priority, so it goes first. If the cell is still over 80% when all the water is gone, it will go to the next lowest priority, which is oxygen, and excrete that. It will only stop when the vacuole is under 80% again.

---

Also, something I discussed with Psychochef wass the concept of Transport Rate and Transport Weight. Transport Rate, as I mentioned earlier, and as crovea called a "bandwidth" for cells, is basically how many units of compounds a cell can take in or out at a time. Think of a room with a bunch of doors. If only one person can enter or leave the room at a time per door, and there is a certain amount of doors, there is a limit to how many people can be entering/leaving the room at the same time. This in Thrive is called Transport Rate, in units/second. Each exposed hex face would increase this rate by X units/second.

However, something I wanted to add in was the idea of Transport Weight. Each compound has transport weight as a property (but it wouldn't matter for compounds not found in the microbe stage). When a molecule of a compound is transported into or out of a cell, instead of just taking up one unit of space, it would take up as many units as it had transport weight. For example, if a cell has a transport rate of 10 units/second, and compound X has a transport weight of 2, then each second the cell could only take in or eject 5 molecules of compound X. What do you think about this feature? Too complex? It adds in the fact that molecules like glucose take longer to be picked up than other molecules.

Lastly, I did get a suggestion from one of the other users that we should create a prototype or demo of this first, playtest it, and see what the results are and find the best solution in that manner.

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PostSubject: Re: Microbial Compounds and Organelles   Fri Nov 08, 2013 1:53 am

Glad to see there's good work being done while I'm being forced away from inventing cellular metabolisms due to my requirement to study them.
I have yet to read much of the new content on this thread, But I like Nick's option A for vacuoles; it's a lot more realistic to expel things down to equilibrium somewhat simultaneously rather than expel them in sequence.

On the concept of Transport Weight: I really, really like this idea, since it takes into account the extra time needed for active versus inactive transmembrane transportation. I think it's probably worth implementing, and also very easy to implement, given that we already have MWs for compounds since they're real-world chemicals. However, I think it can be shelved for a later release.

After reading the thread, I can contribute to discussion.
Nick wrote:
urrently, a mitochondrion could produce 3800 ATP in one timestep, provided it had 600 oxygen and 100 glucose.
Unless I've missed a revolution in the way we model organelle processes, this should not be an issue, since a basic tenet of how organelles work is that every organelle has a certain rate at which it can create its products.

On surface area:
A simple linear function of surface area should be sufficient to determine crossmembrane compound traffic.
Also, it occurs to me that we may not have defined any basal storage in organisms, which is a significant flaw in game design. What I mean here is that each hex used in creating an organism should be able to store a small amount of compounds, and open hexes should be allowed to store significantly more than ones occupied by an organelle. The function of a vacuole remains: it can store significantly more than the 7 hexes it occupies could store regularly.

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PostSubject: Re: Microbial Compounds and Organelles   Fri Nov 08, 2013 6:10 am

NickTheNick wrote:
Lastly, I did get a suggestion from one of the other users that we should create a prototype or demo of this first, playtest it, and see what the results are and find the best solution in that manner.
*cough* probably me^ *cough*
I think Nick and I came to the conclusion that pretty much even if transport weight and such were factored in, the concentration of certain things would be insignificant enough in most cases to make a difference. For example: you wouldn't find the cell saturated in glucose, allowing an insane rate of transfer, even though this doesnt reflect real life situations. Because A) you dont find a cell saturated in glucose B) the cell doesnt require that much glucose for its functions(so would never require said transport in the first place). So even if the transport weight were implemented, there would be no noticeable difference, since there wouldnt be a situation where all the hexes are being overused by large molecules. But, maybe we're wrong, so why not just release something and then if needed implement it, was the gist of things.


~sciocont wrote:
On the concept of Transport Weight: I really, really like this idea, since it takes into account the extra time needed for active versus inactive transmembrane transportation. I think it's probably worth implementing, and also very easy to implement, given that we already have MWs for compounds since they're real-world chemicals
I'm glad someone else liked our idea. We were going exactly for distinguishing Active transport vs basic gas diffusion. Just a quick thought on MWs and its relation to Transport Weight "values". Nick originally suggested we call it just Molecular Weight Values(or something similar) but my concern was that Molecular Weights are not the only significant factor in transport rates. and since we know (and can control) exactly how each basic element (or whatever its called) acts, we can give it values that reflect the other factors. Ex: Gases diffuse, liquids commonly go via osmosis, and solids generally need some sort of protein bridge or whatever. Would glucose be transported as fast as sodium/potassium pumps? because their MWs are like extremely different. I feel like assigning it solely based on MW would be a bit weird when it comes to certain situations (but MW should be a big factor).
Anyways, now im kinda excited for my advanced cell biology course next semester...
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PostSubject: Re: Microbial Compounds and Organelles   Fri Nov 08, 2013 6:35 am

I'd just like to interject here that any mechanism we think up here should still be somewhat easy to understand for players. If the rules underlying a gameplay mechanic are too complex, the mechanic is "just there", without offering interesting decisions to the player. Take Nick's solution A for example. The player sees that his microbe is losing CO2 although the storage organelles aren't completely full yet. So he stops gathering CO2 from the environment. A minute later, glucose is over the ratio and the microbe starts losing glucose instead of CO2. As a player, I would probably think "WTF" at that point. Not to mention that nothing indicates that it's now okay to pick up CO2 again. Most likely, the player will resign to his fate, accepting the continuous loss of resources as a fact of life.

That said, it's not much use worrying about scenarios like this until the mechanic is playtested. To that end, I strongly recommend anyone with gameplay ideas like this to go through some basic Lua tutorial, look through our current scripts and ask questions about them until you have a basic understanding of how they work. Experiment around, change some stuff and see how it affects the game. That's the main reason why we put Lua scripting into the game, so that changing game logic is as accessible as possible.

The reality is, part of the ideas here will always be lost in translation. I (or the other programmers, for that matter) can read through suggestions and try to implement them, but inevitably, I'll come across some snag. Some detail that wasn't specified by the originator of the suggestions. The solution to that snag might be obvious to them, but not necessarily me. At that point, I'll either have to ask them and wait until I get an answer, or make a judgement call and implement a solution myself, which might not fit into the original vision.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Nov 10, 2013 4:27 am

@~sciocont

It wasn't an issue, per se, it was more that I was just posing that problem to follow it up with an explanation of limiting the processing power of organelles. However, nowhere did it specify the rates of organelles, so we are using arbitrary units for now, in which the formula for each process is also the max processing power of each process.

That is a good point that I hadn't considered on alternative means of storage. Here are some numbers to begin with (I really have no idea what it should look like so please correct where if possible):

Each unoccupied hex in a cell gives +10 units to the storage capacity of the cell.
Each occupied hex (that is NOT occupied by a vacuole) gives +4 units to storage capacity.
Each hex occupied by a vacuole gives +20 units to the storage capacity of a cell. (A vacuole has a fixed shape)

@Nimbal

That is a true point, and we would have to somehow convey to the player that an overabundance of compounds is storage will start excretion of necessary compounds. However, for now, I think we should stick with all products immediately being teleported out of the cell (yes, I know it's not realistic). However, we also finish the concept for Solution A, plus the extra stuff on transport rates and transport weights, and we introduce that in a demo or prototype for playtesting. If playtesting gives us a positive result with Solution A, we stick it into the game itself.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Nov 10, 2013 8:27 am

Hi all, sorry I've been away from these discussions for so long.  I'd like to add my thoughts to whats here, but before I disrupt something that's been previously agreed, have we at some point decided that compounds will only be dealt with in integer amounts (for storage, reactions etc.)?  And if so, why?

The reason I ask is that some of the recent discussion seems to be working around this constraint.  E.g.: Nick's option A talks about removing a unit of the most abundant element, or one at random, to reach an optimum ratio.  If compounds weren't being dealt with in integer values (i.e.: you could have fractions of a compound unit), then it would be significantly simpler to remove a fraction from each compound, relative to how far over the optimum ratio that compound is.

I'll also say that as originally planned, the compound system allowed fractional compound units.  If it seems unrealistic to have 0.25 of a glucose unit, keep in mind that the actual unit we're using is (iirc) pico-moles of compounds, which means that each unit represents approximately 6e11 individual molecules.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Nov 10, 2013 6:09 pm

I don't remember why integers were being used, and decimals does make more sense to me, so I agree we should go with that.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Nov 10, 2013 6:30 pm

I was talking about how compounds are dealt with behind the scenes, not whats presented to the player.  Whether we show the player a floating point number or rounded integer, or a percentage, doesn't really affect the mechanics behind compound interactions.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Nov 10, 2013 7:15 pm

Basically, what Seregon is saying is that the units we are using for measuring compounds in the Microbe Stage should allow for decimals, because each unit in Thrive is equal to one pico-mole.

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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 18, 2014 1:25 pm

[quote="Narstak"]One organe that could be interresting is a pocket organe which can store drone-like organismes.

The mother cell would have room for a limited amount of drone-cells.
And to gain those drone-cells, the player have to make them grown, like a plantation.

X quantity of drone-cells = X ressources (minerals and other things + energy)

The drone-cells can:
-attack other cells
-protect the mother cell
-Extend the perimiter of action
-Help to assimilate new DNA more quickly.
-But, in exchange, the mother cell give her protection and use her ressources and energy to repear the injured drone-cells. Fortunatly, the mother cell also take advantage of the situation by having less work to do than on her own.

By leaving the pocket organes, the mother cell will be less defended. If all drone-cells are launch, the mother cell will be vulnerable if the drone-cells went to explore.

This organe need special way to be achieve, or a specialisation.

In evolution, this make the future multicellulare organism less vulnerable to sickness and stronger. Also heal quicker.

I make a concept. I post it:
Concept:
 
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Tarpy
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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 18, 2014 3:45 pm

Narstak, double-posting is against the rules, especially if the second post is nearly identical to the previous one. If you want to add something to your previous post, just edit it.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 18, 2014 4:31 pm

It's a accident...
Sorry...
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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 18, 2014 5:42 pm

I have never heard of such a thing in cellular biology. Can you give some sources? Also, this doesn't sound like a very good or coherent idea.

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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 18, 2014 11:11 pm

In the documentary, The future is wild, there is a species of Jellyfish like creature (call the Ocean Phantom) which contain sphere-like pocket on his tentacules. Those contains colony of cluster-like creature that attack the one who threat the mother ship which the creature is.

There was also a similar concept in Spore in Cell stage. It was a herbivore which realease little carnivore from layed eggs.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 18, 2014 11:39 pm

I hate to cut in, but the Ocean Phantom is not a collection of cells, it is different organisms in a complex symbiotic relationship, and it releases crabs that live inside it. Secondly, the cells in Spore are more like very tiny multicellular creatures, and that is in no way related to your concept.

However, your idea intrigues me. What about using it as a sort of symbiotic relationship at the microbial level? Where say photosynthetic cells live inside the vacuoles of an otherwise carnivorous cell, and provide it with extra ATP? Or a photosynthetic cell could provide some free ATP to carnivorous cells in exchange that the host cell gets protection?

That is a rather big leap of intelligence for a simple cell though.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 3:02 am

That could actually work really well for the transition between the cell stage and the aquatic stage. In the cell stage the player evolves his cell until he gets to a point when he can start creating symbiotic relations with other cells, using a behavior editor of some sort, this will lead to a formation of webs of different organisms that working together manage another bigger organism. For example, before proceding to the next stage you have to find five different cells that are essential for living and 'befriend' them. Itms.
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PostSubject: Re: Microbial Compounds and Organelles   Today at 4:03 pm

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Microbial Compounds and Organelles
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