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 Microbial Compounds and Organelles

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Raptorstorm
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PostSubject: Re: Microbial Compounds and Organelles   Wed Dec 19, 2012 7:34 pm



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

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PostSubject: Re: Microbial Compounds and Organelles   Wed Dec 19, 2012 7:48 pm

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.
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PostSubject: Re: Microbial Compounds and Organelles   Wed Dec 19, 2012 8:58 pm

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.

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PostSubject: Re: Microbial Compounds and Organelles   Wed Dec 19, 2012 9:01 pm

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.

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PostSubject: Re: Microbial Compounds and Organelles   Thu Dec 20, 2012 3:27 am

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?
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PostSubject: Re: Microbial Compounds and Organelles   Thu Dec 20, 2012 12:26 pm

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.
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PostSubject: Re: Microbial Compounds and Organelles   Thu Dec 20, 2012 1:57 pm

Then we are starting with eukaryote cells? Everywere i saw a reference to that, everyone said we were starting with prokaryote cells.
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PostSubject: Re: Microbial Compounds and Organelles   Fri Dec 21, 2012 9:08 am

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.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Dec 22, 2012 8:36 pm

how would a selectly permeable membrane work in thrive?


(Selectivly permeable membrane is when certain nutrients pass when others such as sugar doesn't)
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PostSubject: Re: Microbial Compounds and Organelles   Sat Dec 22, 2012 8:42 pm

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.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Dec 22, 2012 8:44 pm

sounds good to me

next question what about osmosis?
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PostSubject: Re: Microbial Compounds and Organelles   Sat Dec 22, 2012 9:56 pm

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.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Dec 23, 2012 10:03 am

actully osmosis is a huge part in the life of a cell
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PostSubject: Re: Microbial Compounds and Organelles   Sun Dec 23, 2012 3:11 pm

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.

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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 02, 2013 8:24 pm

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.

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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 05, 2013 3:56 pm

You guys are forcing to to triple post here, please participate.

Some more organelles to add to the list, Chloroplasts and Thermoplasts. Did you get to researching those two scio from a while back?

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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 05, 2013 5:04 pm

Well, we alredy have a list of organelles, on the page before this one, so we dont need to list them again. The only think to do is to define them exactly:

  • What compounds does it intake
  • What compounds does it produce
  • What conditions affect that intake or production (moving increases intake of energy, more light means more production of glucose)
  • What they cost to create/what can you get from recycling it/eating it from another cell
  • Any other important fact, like positioning (inside the cell, at the border, or sticking out) or any pre-requisites


I'll copy the list of organelles here, so anyone reding this can find it easily:

Spoiler:
 
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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 05, 2013 6:08 pm

Oh, I hadn't noticed there were organelles listed after the cell types. Man, that's awesome!

When I get back I'll take a look with what you said in mind.

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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 05, 2013 8:22 pm

Now tht i think about it, we also need for the organelles the rate at wich they exchange compounds, how fast they do so and what conditions affect that rate/speed, if any.
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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 06, 2013 2:27 pm

And what compounds they use.
That protocell list is going to disappear soon, I think, but the organelles related to it are useful to know about.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 06, 2013 2:41 pm

~sciocont wrote:
That protocell list is going to disappear soon, I think,

What do you mean?

Also, in terms of propulsion, how do cilia and flagella move the cell differently? Or do they?

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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 06, 2013 5:20 pm

NickTheNick wrote:
~sciocont wrote:
That protocell list is going to disappear soon, I think,
What do you mean?
Ok, here's my promised bigpost.

The current protocell list is woefully unscientific, and, though endocytosis is a good method (most likely the only method) for getting things like chloroplasts, mitochondria, and our thermoplasts, it doesn't really work for things like Cilia, lamellipodes, etc. Thus we need to structure microbe stage more like multicellular stage where mutation, not endocytosis, drives evolution. The current protocell list details almost all of the parts we would need in a cell editor to design a vast array of functioning protists, so we shouldn't ditch it. It's just that an individual flagellum cannot function without a cell to support it, so it shouldn't be swimming around in the world alone.
I'm going to rewrite the current protocell list here and reclassify protocells into traditional organelles and assimilated organelles, and things that we can ditch altogether.

Spoiler:
 
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 my attemt to make cell stage organelles sensible and scientific. Please add your thoughts.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 06, 2013 9:58 pm

So when the player first starts, do they start with a cell that has a membrane loose enough to allow for pseudopodic movement?

How will quantities of compounds that are stored by the cell be measured? What units?

What do you mean by a chance of symbiosis?

Also, I think we should list what organelles and abilities the cell starts with, along with what compounds it can consume, for reference.

And what are the instincts for a cell at this stage? This is what I got.

-Nourishment
-Energy

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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 06, 2013 10:52 pm

NickTheNick wrote:
So when the player first starts, do they start with a cell that has a membrane loose enough to allow for pseudopodic movement?

How will quantities of compounds that are stored by the cell be measured? What units?

What do you mean by a chance of symbiosis?

Also, I think we should list what organelles and abilities the cell starts with, along with what compounds it can consume, for reference.

And what are the instincts for a cell at this stage? This is what I got.

-Nourishment
-Energy
I think we should start them out with a flagellum, but it doesn't really matter. Quantities of compounds-I'm not sure. I want to say that Seregon and I decided on moles, but I'm not sure, since we're dealing with very small amounts, and a mole is way larger than anything we'll be stuffing into the cell, no matter the material.
When you engulf things, you eat them. However, there is a small chance that you will not successfully digest them, and they will become part of your cell (endosymbiosis)
The cell should start out with a nucleus, simple cytoskeleton, and a basic golgi apparatus and ER. Finally, they get a flagellum or some cilia.

What do you mean by instincts?

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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 06, 2013 11:35 pm

For the organism editor UI, there are some tabs called "Instincts", with Nourishment, Energy, and Health being among them. Kind of like stats for an MMORPG. I thought they would be called the same for the microbe stage, because it is still organism mode.

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