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 Microbial Compounds and Organelles

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Immortal_Dragon
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 9:27 am

Actually, the approach insofar has been using a gluer part that allows the player to attach another copy of their cell onto the original for multicellular transition.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 1:44 pm

But if we use a gluer part we would result in an organism made of the same cells. Take the simplest eartworm, it has blood cells, a digestive system with cells creating enzymes, cells for movement, photosensitive cells for eyes...
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 2:38 pm

Actually, what you are talking about is cells differentiating into their specialization, rather than different cells working together. That's what Thrive is simulating, even if it is abstracted out. That's what stem cells are, the same cells that then differentiate into specialized ones.

Organelles such as chloroplasts started out as bacteria that were absorbed and then eventually became organelles. This is abstracted in that the player can unlock the part.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 2:43 pm

Oh, ok I see know thanks for clearing that up for me. However aside from stem cells making up most of our body, 70% of the cells are bacteria that are in a symbiotic relationship with us.
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PostSubject: Re: Mircobial Compounds and Organelles   Sun Jan 19, 2014 2:48 pm

Actually, that is abstracted out too due to complexity. Once the player reaches a certain number of cells, they switch over.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 2:50 pm

There is a better explication of the concept.
http://en.wikipedia.org/wiki/Endosymbiotic_theory
I made a concept.
https://www.facebook.com/photo.php?fbid=621759537879204&set=o.182887991751358&type=1&theater
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 3:12 pm

It's a good idea however it needs a bit more thought, an organism of that size would have troubles entering and exiting through the membrane on a regular basis. It worked for the mitochondria because they only had to get in once and if you think about it there aren't that many cells harboring prokaryotes, it happened like 5 times in a few million years, all the other cells containing chloroplasts are just the children of that one primal cell.

On the other hand if these 'drones' were located on the outside of the cell and had a relationship like leaf-cutter ants have with fungus: the drones attack an enemy cell than the player engulfs it and shares some of the food with the drones it could work.

But this would change the game play drastically and move it away from the standard biological cell world. It sounds too much like a sci-fi spaceship game.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 3:19 pm

Sure, it is rare, but Thrive can also explore possible way the life could find to thrive.
We should not be affraid of explore realistic concept, even if there is no many exemple on Earth.

But this could be a really hard achievement to get. This pocket organe could be access if the player reach a special skill during the cell stage which would require more time.

I don't know. It's just a concept after all, but possible!
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 5:29 pm

I just got an idea how we could simplify your organelle and make it more realistic.


What if we made an organelle called a Plasmasoid B that worked like the plasma cells in our body and created antibodies that the player could then release? The antibodies would then stick to the enemy and slow him down.

Also, now that we are on the topic of new organelles, are you allowed to upgrade the cytoplasm? A lot of important processes that create energy happen in the cytoplasm, such as chemosynthesis. The cytoplasm also tells the cell when it is time to divide, so an upgrade could speed up reproduction.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 8:52 pm

Narstak wrote:
There is a better explication of the concept.
http://en.wikipedia.org/wiki/Endosymbiotic_theory
I made a concept.
https://www.facebook.com/photo.php?fbid=621759537879204&set=o.182887991751358&type=1&theater

Narstak, what you linked is the explanation of the endosymbiotic theory, which is a theory on how prokaryotic cells evolved into eukaryotic cells. To put it in other terms, this has to do with how cells came to have organelles like mitochondria and chloroplasts. I don't see how this backs anything to do with drone cells residing inside the player's cell. Thrive does push the boundaries of LAWK to allow for alien yet practical forms of life, but fabricating a whole process in cellular biology that adds little to the gameplay is neither practical nor realistic.

@The Creator:

I don't know what a plasmasoid is, but a plasmoid is an astrophysical phenomena. The player's cell will be an animal or plant cell in a primordial tidepool, not fighting off germs like a white blood cell, so antibodies won't be included.

The cytoplasm will not be able to be upgraded, since currently it only performs glycolysis. Reproduction becomes available after long periods of having max capacity glucose and other nutrients in the cell, so cytoplasm won't be involved with that.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 19, 2014 10:36 pm

Fine :oops: 
I see you already think about everything. :P 
I will just watch the process, then.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 20, 2014 3:21 pm

Plasmasoid B was just a random name I made up for an organelle that produces antibodies.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 20, 2014 5:41 pm

^ Didn't antibodies need several types of cells to work? Like antigen presenting macrophages and you know a whole immune system.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 20, 2014 6:08 pm

Well... in our body yes. However antibodies are just molecules that bond to antigens, you need the whole immune system because you want them to only target the pathogens. What I was suggesting was throwing a boomerang and hoping that it would hit the enemy cells before coming back and hitting you.

I see know that it adds to many variables to the game play and would only make it more confusing.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 21, 2014 6:01 am

Do you mean molecules that attack other cells indifferently? Than what's the difference from toxins?
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 21, 2014 12:45 pm

Antibodies bond with the antigens in a cell's membrane, their purpose is to slow the pathogen down so that the phagocites can engulf it. Toxins basically just attack cells by ruining vital organelles.
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PostSubject: Feedback needed!   Mon Jan 27, 2014 7:28 am

Hey everyone, I need feedback!

I've implemented three large changes to the compound system, based on the discussions around page 11 of this thread!


  • Storage organelles (green hexes ingame) are now general storage instead of specialized like before. Meaning an organelle isn't limited to just for example Oxygen anymore, but can hold any mix of compounds. (Empty hexes still does not have storage, this feature will be delayed)
  • Organelles will now try to stay below a threshhold regarding how much they have stored, and slowly eject compounds to maintain it. Furthermore they will always eject useless compounds (atm CO2), see definition below.
  • Each storage organelle now has their own bandwidth amount (maximum X compound units moved per second) which limit processes such as ejecting useless compounds and absorbing external compounds. Some processes ignore the bandwidth limit (such as storing products from process organelles)



Here is a demo with the changes~
https://www.dropbox.com/s/pmtgtv67sq1ulhw/ThriveCompoundDemo.zip
Note that i've included some temporary compound models (placeholder placeholders!) to help you discern which compounds are being ejected.
I have also disabled AI as it is not relevant for this demo.

Regarding compound models: Oxygen look like an X, Glucose look like a Nut/Hex, ATP look like three large balls and CO2 look like a large rectangulair bar.

As a reminder, the current Process Organelle (the grey->purple hex) will take 1 glucose, 6 oxygen and produce 3 CO2 and 36 ATP (water not currently included). It will steal compounds from your microbe as it progresses through its "cooldown"/process time while turning from grey to purple to illustrate how close it is to finishing production, after which it starts over.

Some behavior you might notice in the demo:

  • If you are in the middle of a lot of emitters, and is absorbing compounds very fast, the microbe will eject the compounds it can't absorb fast enough.
  • Once your process organelle finishes its process, your microbe will start expelling CO2, and if filled enough, other compounds to make room for the high priority ATP.
  • Everything you absorb/produce past the maintainance threshhold of 80 will >slowly< be ejected.
  • Everything you absorb/produce past the storage capacity of 100 will be >instantly< ejected


You can't observe this, but with the current system, the more process organelle a microbe has, the faster it will be able to absorb external compounds and eject excess compounds. Which might be worth discussing the validity of.


The ejection system is based on a compound priority system. Currently its just static with the priorities: CO2: 0, Oxygen: 6, Glucose: 5, ATP: 10. So when the storage organelles start going above the threshhold they will eject the lowest priority compounds first. Useless compounds are defined as being something the microbe can't use for anything (CO2 here). If the priority system is good enough, I will make it dynamic, such that modifying the microbe will adjust the priorities.


What we need feedback for is a number of things - Remember that we are focusing on the compound system here meaning the compounds themselves and the microbes way of handling them:


  • Is it realistic enough? Which parts are and aren't?
  • How intuitive/confusing is the system as a whole? Would a player be confused about why things are being ejected
  • Which parts will need a tutorial/information to explain the player whats happening and which things should move from a realistic approach to a simpler one.
  • The compound priority system, how should it work? How does number of process organelles needing a compound and how much they need of that compound affect the priority of a compound in the microbe?


If you have suggestions for a change i can likely quickly change it and create different versions of the "scripts" folder, with changes to the system, that i will then link here.
You will simply need to delete the "scripts" folder you currently have, download the one i link and put that in the ThriveCompoundDemo folder instead.

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Last edited by crovea on Mon Jan 27, 2014 6:01 pm; edited 1 time in total
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 27, 2014 9:26 am

Good work! I am downloading it right now. I would love to help with the coding, and I have been examining the code a bit recently, but due to time restraints and the fact that I never used Ogre or the compound-entity style of programming(OOP is my personal choice), I probably won't be useful until some time passes.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 27, 2014 9:35 am

Good to hear Tarpy The Entity-Component style builds on OOP imposing some restrictions and a way of doing things, so OOP experience is naturally a good start! I didn't have any experience with ogre when i started either, and judging from the template-style of the ogre-code, neither did Nimbal, so thats no requirement. But yeah getting an overview of most of the code is good place to start, either for only C++, only Lua or both!

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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 27, 2014 11:56 pm

Ok, crovea, this looks great. I also agree that water is unnecessary at this time as the microbes are in an aqueous environment. I feel like this is realistic enough, but as time goes on specialized storage organelles will be important to protect against accidental reactions taking place inside the organelle.

I will admit that many people may be confused at the ejection of waste materials, but it will probably look better once the concentration gradient map is integrated, so it just looks like a small concentration of the molecules instead of a huge cluster of individual molecules which all look the same.

A tutorial I don't see being useful for quite some time, as the chemicals in play are relatively simple. We should revisit this in the future after more development and playtesting.

I think the compound priority could work similar to Civilization V's city focus. It stays even by default, but will switch around to ensure survival and to maintain the status quo of the organism, and the player can change this to focus on ATP production (perhaps when in combat or running away), Reproductase production, etc.

This work is looking great!

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 28, 2014 5:19 am

Great work on this demo! I got it downloaded well and it was interesting to test out for a while. There were no bugs or strange behaviours/patterns that I noticed.

crovea wrote:
As a reminder, the current Process Organelle (the grey->purple hex) will take 1 glucose, 6 oxygen and produce 3 CO2 and 36 ATP (water not currently included). It will steal compounds from your microbe as it progresses through its "cooldown"/process time while turning from grey to purple to illustrate how close it is to finishing production, after which it starts over.

It should produce 6 CO2 per reaction.

crovea wrote:
Is it realistic enough? Which parts are and aren't?

I think that the total bandwidth of the cell shouldn't be a sum of all the bandwidths of its organelles. Rather, it should be determined off of the number of open faces of hexes along the cells membrane (i.e. it's surface area).

crovea wrote:
How intuitive/confusing is the system as a whole? Would a player be confused about why things are being ejected

I think it's relatively straightforward. Basically, your cell, like any organism, will intake what it needs, and expel any unnecessary amounts as waste. I think a tooltip on this in future tutorials would be sufficient in explaining it to the player. Also, I think basing the priorities off of ratios as I mentioned back on page 11 (I need to reread that) would make the most sense from both a design standpoint and to the player.

crovea wrote:
The compound priority system, how should it work? How does number of process organelles needing a compound and how much they need of that compound affect the priority of a compound in the microbe?

Another late night has caught me unprepared to answer this question. However I'll go back and read through the discussion on page 11 and give my answer then. Basically it's a system based off of the sum needs of all the organelles.

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 28, 2014 5:41 am

WJacobC wrote:
specialized storage organelles will be important

Hrmm, which kind of specialization are you talking about here? And at the moment, the only reactions that take place are ones that the microbe has a process organelle for. Unless we're going for a super realistic approach i would say that this is fine, but if you want to go for a more realistic approach it would be possible, however the player would probably need some chemics 101 then.

WJacobC wrote:
A tutorial I don't see being useful for quite some time

Oh i totally agree, i simply meant which parts, that are confusing, will need a tutorial in the future and which parts will just need simplification so people can understand it without one.

WJacobC wrote:
I think the compound priority could work similar to Civilization V's city focus.
Interresting, I haven't played civilization myself (Im a Total War guy) but I get what you're saying. Perhaps we should map out which things should be automatic (the things ill be implementing now) and which things the player will be in control of (So we dont have to implement a complicated system for automating it).

NickTheNick wrote:
Rather, it should be determined off of the number of open faces of hexes along the cells membrane (i.e. it's surface area).
Ah yes, this was mentioned before i think, must have slipped my mind. I will wait with implementing this until we get more of a microbe construction/modification system in place.

NickTheNick wrote:
Also, I think basing the priorities off of ratios.
Yes that makes sense as well. How would this interact with what WJacobC said?

NickTheNick wrote:
Another late night has caught me unprepared to answer this question.
It was perhaps a bit of a messy question as well, you pretty much answered the second half of the question in my previous quote. The first part of the question is how priority is affected by two process organelles, both needing oxygen, but with, for example, different ratios of oxygen, what kind of priority does oxygen get then?


Playtesting of this will make a lot more sense when we have a functional microbe editor, but I am implementing a lot of it now, so I just want to make sure I'm heading in the right direction

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 28, 2014 9:14 am

I've been following the development of this for a while now, but until fairly recently haven't had time to really get involved, or keep up with the code. I'm aiming to get more involved now I have time, and will be reading through the existing code over the next week or so.

That said, the compound system is something I'm very interested in, as I helped design one of the original concepts for it. There seem to be a lot of changes to that concept since then, and I'd be interested to discuss why some things are implemented the way they are. I can see a few possible improvements, but I'm not sure whether there's a technical limitation preventing them, or if some of the original design wasn't properly explained. I'm not sure if this thread is the place for such a discussion, as it could get quite involved with the actual code, so it may be worth starting a new thread, or a github issue.

What I've seen so far looks promising, but I won't comment on individual parts just yet.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 28, 2014 10:49 am

What I have made here is a continuation of the efforts made to get the compound system on the right track, so I'll be very interrested to hear what you have to say Seregon!

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 28, 2014 12:35 pm

It's great to see more progress! :D 

The first thing I've noticed is that the frame rate, at least for me with a fairly low end computer, is starting to suffer from the large amount of compound models. For most of the time it's not too bad, but whenever I try to move a large distance quickly, the movement becomes very slightly jolty. And considering that the compound models are certainly going to change (I assume into something more fluid), it might end up becoming a bigger problem.

WJacobC wrote:
I think the compound priority could work similar to Civilization V's city focus.

Thinking about this in relation to agents (which is probably what was meant by specialised storage organelles) to be added later, the distribution and priority of organelles' usage of compounds may start to become a little complicated. If the player's cell has a lot of compound A, no compound B and a lot of compound C, with compounds A and B combining to form ATP and compounds A and C creating a specialised agent, what's to stop the cell from automatically using up all of compound A in creating the agent rather than waiting for more of compound B to be collected so it can make ATP, arguably the more valuable? Priorities set for each processing organelle or compound individually (my strategy game comparison is therefore the priorities for influence distribution in Victoria II  :) ) may be an option, although it could make for a lot more micromanaging.

EDIT: Also, good work getting it on Dropbox - there were a few problems last time with the downloads.

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PostSubject: Re: Microbial Compounds and Organelles   Today at 4:31 pm

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