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 Microbial Compounds and Organelles

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ido66667
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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 16, 2013 9:43 am

Daniferrito wrote:
Wow, thats a lot of things. Try to keep it simple. Or at least understaundable for someone without a degree in biology.

Also, we want to allow any cell to have any combination of organelles. We dont want to stick to existing cells.

@ido: That are simple equations. Anyway, i dont know how the chaos theory fits here.

Well, theoretically it does, but I didn’t meant that I want to use it, I just said that I misunderstood what you said (I thought that you want a really serious simulation of Differential equations).

I also didn't said that they were hard, Just said they aren’t ODE's...

ODE example:

d^2y/dx^2+bdy/dx+cy=r(x)

It is a short equitation but not very simple.

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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 16, 2013 11:41 am

Ido, for the last time, stay on topic, before i have to start deleting your posts.

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PostSubject: Re: Microbial Compounds and Organelles   Sun Jan 20, 2013 10:01 pm

Toughtopay wrote:
Hello, for a brief introduction I will be your local biologist until someone more qualified puts me to shame. Let me get straight down to business.

I read through the entirety of this thread and wrote things down on notepad whenever I had something I can't help but elucidate or explain. It's a long one.

Spoiler:
 


Now that I'm done commenting, here's an important thing I notice has been overlooked: the surface/volume ratio.
This is why you never encounter five meter big amoebas when you go to work in the morning, is that the surface with which you can interact with the environment (gain nutrients) is inversely proportional with your volume. There's a number of ways life has found around that problem, and I could give you more information if that's relevant to the game or just plain interesting.

So I'm here, rather enthused to help, I notice you're interested in compounds you could use as resources necessary for growth and in the different organelles. I'm not sure if that's still relevant and I'm slightly confused as to what exactly you would like to know. For example nowhere do I see mention of the Golgi apparatus, but I do see lyzozymes which are useless without the vesicules secreted by Golgi. Nor do I see the Endoplasmic reticulum which is important for the formation of said lyzozymes.
I like you. Stick around.
Back on the topic of organelles, everyone: what organelles are missing currently? Are there any conceptual organelles you'd like to put forth for review. Remember that the golgi apparatus/ER/vacuoles/lysosomes are standard and need only be upgraded in efficiency.

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 29, 2013 6:41 pm

I don't know of any organelles we're missing. Unless there are imaginary ones that we could add.

~sciocont, I remember you saying something about a hierarchy of organelles where some had to be unlocked/assimilated before others, and, ultimately, the gluers, could be assimilated/unlocked. I couldn't find the post for it, though.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 29, 2013 6:55 pm

MitochondriaBox wrote:
I don't know of any organelles we're missing. Unless there are imaginary ones that we could add.

~sciocont, I remember you saying something about a hierarchy of organelles where some had to be unlocked/assimilated before others, and, ultimately, the gluers, could be assimilated/unlocked. I couldn't find the post for it, though.
Once we have all of the organelles down, we can work out linkages between them, evolutionarily, and how they each use compounds.

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 29, 2013 7:33 pm

So where is the current and most up to date list on the organelles? If someone would post it I would gladly add it to the OP. Did you have one Toughtopay?

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 29, 2013 11:17 pm

This should be it.
~sciocont wrote:
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   Wed Jan 30, 2013 12:23 am

Ahh, perfect! I'll get to adding this to the OP tomorrow, when I have time.

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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 30, 2013 10:33 pm

Please don't quote such a huge post. -NickTheNick

Hold on, how will we get the orange ones? Will they be available in the editor, or will they be a random cell part given by a mutation after reproduction and there won't be an editor? Is there a random chance we'll start up the editor and it'll be unlocked?
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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 30, 2013 10:40 pm

You have a chance of assimilating (terminology?) them into your cell each time you consume one.

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PostSubject: Re: Microbial Compounds and Organelles   Thu Jan 31, 2013 11:28 am

~sciocont wrote:
Orange numbers are now organelles that can be gained through mutation and not through endocytosis.

Green numbers can be achieved through mutation or engulfment.

Blue numbers can be gained exclusively through endocytosis.
Nick - Endocytosis/engulfment seem to be equivalent to assimilation, in which case blue numbered organelles have a chance of being gained when you consume the related proto-cell. Orange ones can be gained through mutation, and green can be gained in both ways.

In response to the question, mutation would occur through gameplay, examples I can think of being through a copying error (in reproduction) or random mutation. The parts will also be in the editor, though - the player will (eventually) have the option to apply manual edits upon reproduction (with/without limitations to change) using the microbe editor, and hopefully we will also get a microbe directional editor (causes gradual mutation towards a goal) working, if we ever get around to it.
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PostSubject: Re: Microbial Compounds and Organelles   Thu Jan 31, 2013 7:43 pm

MitochondriaBox wrote:
Please don't quote such a huge post. -NickTheNick

Hold on, how will we get the orange ones? Will they be available in the editor, or will they be a random cell part given by a mutation after reproduction and there won't be an editor? Is there a random chance we'll start up the editor and it'll be unlocked?
Anything orange there arises from random mutation- you'll see it show up available for your use in its most basic form in the editor with no warning.

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PostSubject: Re: Microbial Compounds and Organelles   Sat Feb 02, 2013 12:20 pm

Hey. Sorry about disappearing, I've been swamped. I finally got to a point right now where I'm on top of things again, so I'm once again throwing away what could be relaxing free time in order to help out with what I hope will eventually become a new source of relaxation I'll be ignoring when I have down time in the future.

I have all the info in my binders, I'll update my organelle table so you can get a nice condensed pdf with all the information (weight (insofar as it's possible to give an approximation), composition, sizes, volumes, real life functions) for use when you define the different organelles with code. So I suppose this should be up before the day is done for me.

EDIT: I've done significant progress. Weight is the only thing I can't seem to figure out. I'm going to need you guys to help me out with deciding how to do this. I was thinking what would happen is I would give you volumes and their associated weight as well as percentages of what the organelle is composed of and then you could code in that "1cm^3 of X weighs M and needs this much protein and this many lipids". But I can't find weights. I just can't do it.

In any case, here's the new version, much improved over the last and I'd even say nearly complete : https://docs.google.com/file/d/0B6c9x8zUW_2sS2YtYmFLd3lVS1E/edit?usp=sharing
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PostSubject: Mass of a cell   Mon Feb 04, 2013 12:41 am

We love you. This will be immensely useful as we figure out how to work organelles.
This paper Puts the mass of a human cell at 1.139± 0.003 g/cm3. That should be good for what we do, we can round it down to 1.3 since I'd suspect a free-living eukaryote to be less dense than a human cell, and the paper puts an e.coli cell density at 1.160± 0.001 g/cm3.

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PostSubject: Re: Microbial Compounds and Organelles   Mon Feb 04, 2013 3:20 am

I did not think of going that route!

Also, to help make that slightly more complete we might make use of this table from my biochemistry class:

Percentage of total mass:

70% Water
18% Proteins
5% Lipids
0.25% DNA
1.1% RNA
2% Sugars
1% Ions
3% Monomers

Oh, and 1.3 would be rounding up. Although I didn't read the article yet so maybe the typo is in 1.139. I love you guys too.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Feb 04, 2013 9:26 pm

Toughtopay wrote:
I did not think of going that route!

Also, to help make that slightly more complete we might make use of this table from my biochemistry class:

Percentage of total mass:

70% Water
18% Proteins
5% Lipids
0.25% DNA
1.1% RNA
2% Sugars
1% Ions
3% Monomers

Oh, and 1.3 would be rounding up. Although I didn't read the article yet so maybe the typo is in 1.139. I love you guys too.
Ok, great. That's why it's good to have a lot of people from different backgrounds on a problem, we can quickly find solutions.
1.39 rounded up is 1.4- in "rounding down" I assumed the eukaryotic cell density would be similar to human cell density, so I rounded down from the 1.39 reading to a less dense measure of 1.3 (1.30)
That makes sense, right?

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PostSubject: Re: Microbial Compounds and Organelles   Mon Feb 04, 2013 9:55 pm

~sciocont wrote:
...
mass of a human cell at 1.139± 0.003 g/cm3
...
e.coli cell density at 1.160± 0.001 g/cm3.

I dont know where you get 1.3 from rounding. Did you meant to write 1.39, or you readed that after you wrote 1.139? That's the whole missunderstaunding here. I believe it is 1.139, as 1.3 on human cells would mean we would sink really fast.

I actually though that an aproximation of 1 would be enough, lacking any better number. If the original numbers are right, having a density of 1.150g/cm3 for all cells seems the right thing to me.
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PostSubject: Re: Microbial Compounds and Organelles   Wed Feb 06, 2013 12:14 am

Daniferrito wrote:
~sciocont wrote:
...
mass of a human cell at 1.139± 0.003 g/cm3
...
e.coli cell density at 1.160± 0.001 g/cm3.

I dont know where you get 1.3 from rounding. Did you meant to write 1.39, or you readed that after you wrote 1.139? That's the whole missunderstaunding here. I believe it is 1.139, as 1.3 on human cells would mean we would sink really fast.

I actually though that an aproximation of 1 would be enough, lacking any better number. If the original numbers are right, having a density of 1.150g/cm3 for all cells seems the right thing to me.
Belgium I'm an idiot. I missed that tenths place entirely multiple times. Round to 1.13 about?

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PostSubject: Re: Microbial Compounds and Organelles   Wed Feb 06, 2013 7:52 am


The next prototype able to put a song in the background? like this

http://www.youtube.com/watch?v=i59ZNe_9Wbw

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PostSubject: Re: Microbial Compounds and Organelles   Wed Feb 06, 2013 11:49 am

Yup, that shouldnt be too hard to include. However, try to keep this thread for discussing the organelles and compounds. If you want, ask about this on the "Microbe Stage Progress Report".

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PostSubject: Re: Microbial Compounds and Organelles   Wed Feb 06, 2013 1:48 pm

Alright, I'm going to take a stab at combining everything we have so far, so it'll be rather heavy on math. I suggest we make this the basic template for a microbe, and then add gameplay over it. For example imposing a limit to how much smaller/lighter than that you're allowed to be, etc.

I'll also try and turn the relations into functions. I'm not sure if this is the right place to post this or not, but you'll tell me if it isn't. Plus I can't be more off-topic than the person who linked to an incredibly soothing theme.

Math:

Our subject will be a perfectly spherical cell with the radius R = 5 µm Dear Lord, I forgot there could be other shapes for microbes. I think amoebas are out of the question if we want to take this approach, or we could just give all shapes the same function but different graphics. This isn't really my domain though so I'll leave it at that.

Spoiler:
 

Now that we have a new table with all the masses, the next step is to put that in relation with the different organelles:

Spoiler:
 
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PostSubject: Re: Microbial Compounds and Organelles   Thu Feb 07, 2013 1:07 am

Really, really excellent work.
Given the relative proportions you've calculated, we're well o n our way to defining the entire cell metabolism for the game. Don't go crazy calculating out the volumes of different parts of the cell, because those will differ from organism to organism. We don't need to know how big or how many, just what they're made of (continue with relative proportions) and what they do.

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PostSubject: Re: Microbial Compounds and Organelles   Thu Feb 07, 2013 11:26 am

Thanks, I'm really enjoying my part in the project so I'm glad to see I'm actually of use. I will definitely try and do this for everything, but I'm not sure what you're referring to exactly when you say relative proportions. I mean because the volumes are variable I can't really say 1 golgi = 5 mitochondria. I'm assuming you a mean to continue giving you information such as "The mass of the cell membrane is half lipids and half proteins" but I would like to just double check first.

Now as for my whole bothering with specific organelle volumes, I'm trying to just gather information from everywhere and somehow patchwork it all so that I have a very average cell prototype with everything defined.
This way I can give you (hopefully approximately correct) constants such as the term I defined as Lipid Density. So that when the player "buys" a mitochondria you know how much it costs based on the size the player decides to make it, simply because we assume that it's all going to be proportional.
I also imagine the numbers could be useful for people to have an idea of "oh that's a mitochondria, it's fairly small, look over here there's a big bloated golgi apparatus"

Really lipids are the only thing I needed a volume for because they're just there for membranes (we should not have bacteria who are able and willing to store triglycerides for energy.

Oh and all organelle functions are here. It's the same file I linked two posts ago, I believe. So if you've read that you should let me know if you'd like any more details on any of them.
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PostSubject: Re: Microbial Compounds and Organelles   Sat Feb 09, 2013 12:01 am

Quote :
I'm assuming you a mean to continue giving you information such as "The mass of the cell membrane is half lipids and half proteins" but I would like to just double check first.
That is indeed what I meant

I read your chart a few days ago, now the link seems to not be working- the document isn't showing up. I don't think I had any problems with it though.

All of the volume work you're doing is great, I just want to make sure we're on the same page.

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PostSubject: Re: Microbial Compounds and Organelles   Thu Feb 28, 2013 4:03 pm

I can't believe it's almost been a month already. I don't have any new content to offer, I'm still in the middle of my genetics revisions. There isn't much I could have contributed between then and now; there's definitely some things to add, but not very much. My biochem classes have gone really in-depth about nucleic acids and so have consisted of information which is unusable for the game.

We start lipids next week, and then proteins, presumably going into metabolic pathways and whatnot, so I'll try to incorporate an update into the revision of my notes if I have the time. I'll also be sure to lurk a bit beforehand just in case progress has been made without me.

So this post is just to say I'm not entirely gone yet. I believe I can still provide useful information, I just haven't had much time or a real mass of information to make use of in these past three or four weeks.
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