| Statistics | We have 1675 registered users
The newest registered user is dejo123
Our users have posted a total of 30851 messages in 1411 subjects
|
| Who is online? | In total there is 1 user online :: 0 Registered, 0 Hidden and 1 Guest :: 1 Bot None Most users ever online was 443 on Sun Mar 17, 2013 5:41 pm |
| Latest topics | » THIS FORUM IS NOW OBSOLETE
 by NickTheNick Sat Sep 26, 2015 10:26 pm
» To all the people who come here looking for thrive.
by NickTheNick Sat Sep 26, 2015 10:22 pm
» Build Error Code::Blocks / CMake
by crovea Tue Jul 28, 2015 5:28 pm
» Hello! I can translate in japanese
by tjwhale Thu Jul 02, 2015 7:23 pm
» On Leave (Offline thread)
by NickTheNick Wed Jul 01, 2015 12:20 am
» Devblog #14: A Brave New Forum
by NickTheNick Mon Jun 29, 2015 4:49 am
» Application for Programmer
by crovea Fri Jun 26, 2015 11:14 am
» Re-Reapplication
by The Creator Thu Jun 25, 2015 10:57 pm
» Application (programming)
by crovea Tue Jun 23, 2015 8:00 am
» Achieving Sapience
by MitochondriaBox Sun Jun 21, 2015 7:03 pm
» Microbe Stage GDD
by tjwhale Sat Jun 20, 2015 3:44 pm
» Application for Programmer/ Theorist
by tjwhale Wed Jun 17, 2015 9:56 am
» Application for a 3D Modeler.
by Kaiju4u Wed Jun 10, 2015 11:16 am
» Presentation
by Othithu Tue Jun 02, 2015 10:38 am
» Application of Sorts
by crovea Sun May 31, 2015 5:06 pm
» want to contribute
by Renzope Sun May 31, 2015 12:58 pm
» Music List Thread (Post New Themes Here)
by Oliveriver Thu May 28, 2015 1:06 pm
» Application: English-Spanish translator
by Renzope Tue May 26, 2015 1:53 pm
» Want to be promoter or project manager
by TheBudderBros Sun May 24, 2015 9:00 pm
» A new round of Forum Revamps!
by Oliveriver Wed May 20, 2015 11:32 am
|
| | | Microbial Compounds and Organelles |  |
|
+20Immortal_Dragon Tarpy Narstak Psych0Ch3f Nimbal crovea untrustedlife RodGame Doggit MitochondriaBox Toughtopay ido66667 Rorsten594 Raptorstorm Daniferrito The Uteen ~sciocont Seregon Holomanga NickTheNick 24 posters | |
| Author | Message |
|---|
ido66667
Regular
Posts : 366
Reputation : 5
Join date : 2011-05-14
Age : 110
Location : Space - Time
 | | Subject: 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. | |
|  | | NickTheNick
Overall Team Co-Lead
Posts : 2312
Reputation : 175
Join date : 2012-07-22
Age : 28
Location : Canada
| | Subject: 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. | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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:
Ah, thermoplasts. Alright, so chloroplasts use light for photosynthesis. Thermoplasts use heat for photosynthesis; the idea is that heat emits infrared radiation, which is an electromagnetic wave. So light. It's much less effective to use that part of the electromagnetic spectrum, so it's only useful if it's the ONLY part of the electromagnetic spectrum available. If you've ever heard of "Black Smokers" (hydrothermal vents deep, deep down in the sea) this is pretty much the only place where thermoplasts can be considered to exist. They don't use chlorophyll because..well..why would they? So they're not chloroplasts. Also to my understanding Carbon is replaced by Sulfur in this photosynthetic reaction.
Binary fission is the division of an entire organism into two halves which later regenerate. That means if you have a single cell there's little you can see to differenciate it from mitosis, but once you're talking about metazoans the difference is obvious. A good example of that would be platyhelminthes. So binary fission in procaryotes is mitosis, and it's more complicated than mitosis when it's binary fission for a metazoan.
Gluers. I'm not sure what you mean by that, especially the bit about DNA. As I'm French I assumed in my language the term was just very different from "gluers" but it appears to rather be a word meant to explain the function than the scientific term since on the first page I saw an article about women who glued a man's penis to his abdomen because he was unfaithful. So I will assume you mean the extracellular matrix which keeps different cells together. If it is the extracellular matrix I may have some things to say about that.
You do not need centrioles for cell mitosis. Plants simply don't have them. I'm not too knowledgeable on the subject, but a bit of research could give us something to go.
Respiration is incredibly convoluted if you assume the point is just to get a proton on the other side. But that's not the point. But it's not. The point is to be as long a circuit (for the electron) as possible so that you benefit fully from this free (powered by gradients) source of energy. It would be more convoluted to have a different circuit for each step and evolution doesn't like waste. So again, it's good that it's circuitous because that's more efficient.
Cell walls at a unicellular stage mean that, for gameplay, you'll either need to eventually lose them to reach a (fun) metazoan gameplay, or you'll stay stuck as a microbe/become a plant. A mushroom if you're lucky. Furthermore you mention the importance of silicate but that's pretty much just diatoms. If you're an alga it's mostly about sugars, proteins come into play when the cell is done growing but that's of little importance. Or, you know, have Belgium science. Which is really funny to me as a Frenchman because we often joke about the Belgian as though they were lesser people. Kind of like Americans and Canadians.
You mentioned membranes that act as filters, and suggested it could depend on the size of the nutrients going in, that's entirely true: if your membrane is permeable enough to allow a fatty acid to just waltz through your cell must be torn open. However there is an exception: membranes are not permeable to ions, you need specialized ion pumps. (Water has its own pumps too. Just anything that's charged doesn't get through because a membrane is a lipid bilayer and thus has a hydrophobic core which doesn't allow charged molecules through).
When a mitochondria/chloroplast is assimilated to your cell, you might want to call it endosymbiosis just to be more precise.
Cilia are much smaller (about 10x) than flagella, and they have a second basal body (which you really, really don't need to bother caring about).
ATP gives energy when it's broken into ADP+P, and it takes very little energy to attach that P back to make it ATP again. Actually this is what ultimately happens with respiration, an electron goes around oxydating and all the while activates pumps which expulse protons many steps of the way, which causes chimio-osmosis and the protons comes back through an ATP synthetase.
Finally this last comment is just for my curiosity:
Clone Stickers. I've been unable to find any mention of them on Wikipedia and they seem really interesting.
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. | |
| | | | MitochondriaBox
Learner
Posts : 188
Reputation : 7
Join date : 2013-01-29
Age : 24
Location : Houston, Texas
| | Subject: 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. | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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. | |
| | | | NickTheNick
Overall Team Co-Lead
Posts : 2312
Reputation : 175
Join date : 2012-07-22
Age : 28
Location : Canada
| | Subject: 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? | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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:
1) Wrigglers - Worm-like creatures that move quickly around the screen; assimilating them grants the player a flagellum
2) Writhers - Small globular creatures that move quickly around the screen by rippling cilia on their body; assimilating them grants the player cilia
3) Squirmers - Crescent-shaped creatures that move by undulating themselves up and down like a pair of wings; assimilating them grants the player lamellipodes
4) Squishers - Glob-shaped creatures that move in an amoeba-like fashion, by wriggling their cytoplasm; assimilating them grants the player the ability to move in this way and engulf other cells.
5) Shiners - Small spherical creatures that drift and emit a pale colored light whenever they absorb amino acids; assimilating them grants the player a bioluminescent dot that shines when they feed
6) Clone-Stickers - Tiny globs with a hollow spike (like a hypodermic) that inject their reproductive material into other cells, causing them to die and be replaced by another sticker. Assimilating them grants the player a pilus (hypodermic spike) that can create clones of the player cell in this manner.
7) Poison-stickers - Tiny globs with a hollow spike (like a hypodermic) that inject toxic material into other cells, causing them to die and dissolve into edible material. Assimilating them grants the player a pilus (hypodermic spike) that injects poison.
Defenders - Tiny capsules that resist being absorbed by cells; assimilating them grants the player an antiphagocytic capsule which defends them from being absorbed by other cells by producing an outer coating of enzyme "slime"
9) Producers - Blobs that cluster around rich regions of the soup, transforming the amino acids into proteins. Assimilating them grants the player double nourishment from absorbing Amino Acids, and allows damaged cell components to be replaced.
10) Dissolvers - Blobs that cluster around proteins and reduce them to amino acids. Assimilating them grants the player double nourishment from absorbing Protein, and allows cells with Walls to be consumed.
11) Eaters - Small globes that absorb proteins and other cells, converting them to energy for reproduction; assimilating them grants the player Mitochondria, which allows them to "eat" carbohydrates.
12) Light-eaters - Small discs that reproduce automatically while exposed to light; assimilating them grants the player Chloroplasts, which transform light into nourishment (carbohydrates)
13) Heat-eaters - Small blobs that reproduce automatically when exposed to heat; assimilating them grants the the player Thermoplasts, which transform heat into nourishment (carbohydrates)
14) Cookers - Small spheres that release enzymes which break down proteins and cells into amino acids; assimilating them grants the player Lysosomes, which give double nourishment from consuming Cells
15) Holders - Hollow membranes that encase whatever molecules they come in contact with; assimilating them grants the player Vacuoles, which can store material to be digested, or compartmentalize harmful substances (like poison or injected reproductive material).
16) Platers - Solid "plates" that reproduce by absorbing proteins; assimilation grants the player Cell Walls, which 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).
17) Gluers - Globs that create a sticky enzyme that can glue cells together. Assimilating them grants the ability to bond with other cells of your type.
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. | |
| | | | NickTheNick
Overall Team Co-Lead
Posts : 2312
Reputation : 175
Join date : 2012-07-22
Age : 28
Location : Canada
| | Subject: 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. | |
| | | | MitochondriaBox
Learner
Posts : 188
Reputation : 7
Join date : 2013-01-29
Age : 24
Location : Houston, Texas
| | Subject: 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? | |
| | | | NickTheNick
Overall Team Co-Lead
Posts : 2312
Reputation : 175
Join date : 2012-07-22
Age : 28
Location : Canada
| | Subject: 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. | |
| | | | The Uteen
Sandbox Team Lead
Posts : 1476
Reputation : 70
Join date : 2010-07-06
Age : 27
Location : England, Virgo Supercluster
| | Subject: 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. | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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. | |
| | | | Toughtopay
Newcomer
Posts : 15
Reputation : 2
Join date : 2013-01-13
Age : 29
Location : France
| | Subject: 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 | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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. | |
| | | | Toughtopay
Newcomer
Posts : 15
Reputation : 2
Join date : 2013-01-13
Age : 29
Location : France
| | Subject: 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. | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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? | |
| | | | Daniferrito
Experienced
Posts : 726
Reputation : 70
Join date : 2012-10-10
Age : 30
Location : Spain
| | Subject: 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/cm 3 for all cells seems the right thing to me. | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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? | |
| | | | Doggit
Regular
Posts : 444
Reputation : 36
Join date : 2012-04-28
| | Subject: 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
https://www.youtube.com/watch?v=i59ZNe_9Wbw
| |
| | | | NickTheNick
Overall Team Co-Lead
Posts : 2312
Reputation : 175
Join date : 2012-07-22
Age : 28
Location : Canada
| | Subject: 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". | |
| | | | Toughtopay
Newcomer
Posts : 15
Reputation : 2
Join date : 2013-01-13
Age : 29
Location : France
| | Subject: 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:
Cell Density is 1.13 g.cm^3 so 1,13*10^-12 g.µm^3 and cell volume is Vcell = (4*Pi*R^3)/4 = 523.6 µm^3
Therefore Mcell = 1.13*523.6*10^-12 = 5.916*10^-10 g <=> 591.6 pg
If we cross-reference with the table I posted above, we see that we have:
MH20 = 591.6*0.7 = 414.12 pg
Mproteins = 106.488 pg
Mlipids = 29.58 pg
MDNA = 1.479 pg
MRNA = 6.508 pg
Msugars = 11.832 pg
Mions = 5.916 pg
Mmonomers = 17.748 pg
We can divide all of the polymers which are necessary to life into four categories (as I will later be explaining in my next update of the compounds list):
Proteins, Lipids, Sugars and Nucleic Acids
Here we have 3% of just "monomers", and I don't have any more information. They could be monomers for anything, and it's a fair amount because we only have 5% of lipids and 1,35% of nucleic acids. So it's an important value. I suggest going the safe route and just giving each class of polymers an mass of monomers proportional to its own total mass.
So we have:
Mproteins = 106.488 pg
Mlipids = 29.58 pg
Msugars = 11.832 pg
M-NA = 1.479 + 6.508 = 7.987 pg
Thus Mpolymers = 155.887 pg
%proteins = 68.3%
%lipids = 18.97%
%sugars = 7.6%
%-NA = 5.12%
And finally we can find out how many monomers each polymer class requires:
Nproteins = 17.748*0.683 = 12.12 pg
Nlipids = 3.36 pg
Nsugars = 1.35 pg
N-NA = 0.908 pg
So we have a new table:
MH20 = 414.12 pg
Mproteins = 106.488 pg
----Nproteins = 12.12 pg
Mlipids = 29.58 pg
----Nlipids = 3.36 pg
MDNA = 1.479 pg
MRNA = 6.508 pg
----N-NA = 0.908 pg
Msugars = 11.832 pg
----Nsugars = 1.35 pg
Mions = 5.916 pg
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:
For example we know that lipids have for main purpose to make up membranes. Unfortunately it's not as simple as saying lipids = cell membrane, because the cell is like a big bag of membranes. There's the cell in its entirety, the nucleus, the endoplasmic reticulum, the golgi apparatus and the mitochondria.
So, I already calculated this cell's main membrane volume earlier and came up with
Vpm = 1.25 µm^3
Vnucleus = 65.45 - 65.13 = 0.32 µm^3
Ver = Between 150 and 250 µm^3 ? (Guesswork)
Vgolgi = Between 100 and 200 µm^3 ?
Vmit = 4 - 3.96 + 0.1 = 0.14 µm^3/mitochondria (the +0.1 is for trying to compensate for being unable to calculate the folds and whatnot))
I suggest that, if we want accurate numbers for Golgi and the ER (as well as mitochondria) I can get electron microscope images and we could make generalizations off of the numbers we get from that. I'm having a pretty hard time visualising it, especially since I don't have any accurate 3D representations. I'll ask my cellular biology teacher next time I have class for an estimate.
Nevertheless, I promised a function and while the numbers might change, the concept will stay the same:
First we need to define lipid density LD = Mlipids/(Vpm + Vnucleus + Ver + Vgolgi + Vmit)
Now we can have a function that determines how much more membrane you can create
LipidLevels - (Vpm + Vnucleus + Ver + Vgolgi + Vmit)*LD = MembraneLeft
So the only things that may change are the "lipid prices" of different organelles and the LD constant. Another important thing to note is that the plasmic membrane's mass is 50% proteins, but proteins are outnumbered 50 to 1, so the volume depends on lipids, but you'll theoretically have to use up just as much protein mass.
We can have many other functions, but I just wanted to start the ball rolling on that.
And finally I just found http://jcb.rupress.org/content/55/2/524.full.pdf which could be immensely useful, especially after briefly taking a look at p.4 of the pdf. But I'm beat for today.
| |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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. | |
| | | | Toughtopay
Newcomer
Posts : 15
Reputation : 2
Join date : 2013-01-13
Age : 29
Location : France
| | Subject: 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. | |
| | | | ~sciocont
Overall Team Lead
Posts : 3406
Reputation : 138
Join date : 2010-07-06
| | Subject: 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. | |
| | | | Toughtopay
Newcomer
Posts : 15
Reputation : 2
Join date : 2013-01-13
Age : 29
Location : France
| | Subject: 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. | |
| | | | Sponsored content
| | Subject: Re: Microbial Compounds and Organelles | |
| |
| | | | | | Microbial Compounds and Organelles | |
|
Similar topics | |
|
| | Permissions in this forum: | You cannot reply to topics in this forum
| |
| |
| |
