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 Microbial Compounds and Organelles

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ido66667
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PostSubject: Re: Microbial Compounds and Organelles   Sat Jan 12, 2013 10:55 am

Daniferrito wrote:
F = p ???

p is momentum, or kinetic energy, which is a totally different thing.

Anyway, i believe we are getting too OffTopic. This is not a good topic for this.

Sorry, v withount a small line of it the the instantaneous velocity, and the devertive of the instantaneous velocity is a... My bad.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 14, 2013 7:03 am

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.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 14, 2013 10:25 am

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.

Hey!

Happy to see that we have a biologist in here!

I think we talked about it once in some thread when someone talked about creatures big as biomes.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 14, 2013 10:44 am

I'm happy to be here. That's good then, I imagine it could make for good resource management if you incorporate the aspect of "If you're too big you can't feed yourself fast enough to survive". I don't know how much of a headache it'll be but a common way for organisms to solve the problem is to have many folds, encourage concave forms or even have "holes" to be bigger but not as voluminous, if that's a word in English.

I will be contacting Seregon to let him know I'm here to help then. Fun fact about creatures as big as biomes, actually, Armillaria is a mushroom which has infected 47 000 trees. That doesn't mean there's one gigantic mushroom overlooming a forest, but there's a good 5000 tons worth of mushroom heads in a gigantic network (the "roots").

And I thought a 200 ton whale was massive.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 14, 2013 1:32 pm

That problem/idea (surface/volume ratio) has been raised a few times alredy. Especially its similar question, how to prevent evolved animals into geting incredibly huge. It's quite easy. bigger muscles/organs (or organelles, or whathever the creature is composed of) means it will need much more food (ratio goes up cubically, if that is a word, but food income doesen't).

On a small scale, it will mean that the individual will need to eat more, more often, leading to having to be hunting for food all the time. On a bigger scale, the more energy (food) a species needs to intake (because of bigger body), the less energy it will be remaining to make successors (and each successor will need more energy to be formed too), so as birth-rate suffers, population decreases.

That is the way a creature can't grow too big. In our particular case, the cell wont be able to find all the food to feed on, and it will take more time to absorb it.

Similar things happen with photosyntesis. When radius doubles (x2), intake goues up by four (x22), but energy in order to keep alive (basal metabolic rate?) goes up by eight (x23)

About your other points:
  • Gluers: Yes, however it happens, what we call gluers are the things that make multiple cells keep together.
  • Binnary fission: Still, apart from the name-change, and being more complicated to undertaund, what else do we need know?
  • Cillia and flagela: Great!, its the first time someone said what they are diferent on. That means that you need multiple cilia in order to perform the task of a flagela. Which method is more efficient?
  • Thermoplasts: Althrough lower radiation could be a source of energy, raw heat can be too. It seems more logical. Most reactions that intake energy do through heat, and most that produce light do as a byproduct of the heat generated (At least the ones i know, im a math/computer guy, not a chemist)
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 14, 2013 3:19 pm

Hi Tought, welcome to the forums. This is partially a reply to your PM, but also to the recent posts here. Hopefully I can give a little more detail on what it is we need to make the compound system work. I'm sure this has been posted somewhere before, but I doubt I'd be able to find where.

Most of the work I've done has been on creating the actual compound system (see here), which is how the computer will deal with whatever list of compounds and processes we throw at it. What we need to work on now is a list of compounds (e.g.: water, oxygen, sugar, protein), processes between those compounds (e.g.: glycolysis, aerobic respiration, photosynthesis, protein synthesis (translation), etc.), and the organelles required to do so (mitochondria, chloroplasts, RER etc.). We have fairly good lists for some of these, but what we really need is details, so for example:

Aerobic respiration:
Input - 1 glucose, 6 oxygen
Output - 6 CO2, 6 water, 38 ATP
Organelle required - Cytoplasm (1 nanoliter), mitochondria (0.5 nanoliter)

Most of the actual reactions are fairly simple, we can just look them up. What we won't easily be able to find are the ATP required for certain reactions, and the amount of organelle space required. I realise that 'space in an organelle' isn't exactly whats being used (in most cases its surface area), so we may want to tweak that, but for now it'll do as a useful measure of how many processes each organelle can support.

Then for organelles we need an idea of how big they can become, what compounds are needed to create them (mainly proteins, phospholipids, cell surface receptors etc.) and in what quantities.


A few comments on your earlier post:
This is far from the only thread dealing with this subject, a lot of what you mentioned has been covered elsewhere (something we really need to work on is getting all of this in one place, probably the wiki).

A lot of our current cell stage is based around endosymbiosis. The idea is that you start with a very basic eukaryotic cell, and gain useful organelles through endosymbiosis, in order to get access to more processes. Some of these organelles (mitochondria, chloroplasts) are realistic, others are ones we've largely invented (gluers, clone stickers - which I think are used to start sticking together more cells and progress to the multicellular stage. Scio recently posted a list of which of these organelles are gained through endosymbiosis, and which through mutation, was that in this thread?

Thats all I can think to say for now (and this post has already taken far too long to write). Let me know any further questions and I'll try to respond later on.
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 14, 2013 4:13 pm

I'm definitely not very knowledgeable on different possible reactions either, as far as I know heat is just...atoms vibrating, so I don't know how that vibration would be absorbed and turned into energy, what I do know is that a person with a PhD who studies procaryotes told me (and a few hundred other students) that there are photosynthetic bacteria near those hydrothermal vents and they use infrared light because they have no choice. That seems to be the closest thing to thermoplasts I can find on the web and in my lectures.

Alright so, bearing in mind what you've told me, here's what you need to know while I make a new list:

EDIT: I just read Seregon's post and the other thread on compounds, I'm getting a pretty clear understanding of what's needed. I'll mull over it tonight and try to figure something out, the main problem being that microbes are powerhouses and the reactions involved are counted by billions. I'll try and figure out some small but representative numbers. I'll leave the rest of the post as is since I should really get to studying for my math test tomorrow and it's still relevant information. Just not as relevant as I thought it was.

Spoiler:
 


Since you view this from a practical standpoint (how much of X does Y provide etc.), I will probably finish it with a comparative table to give you an estimate of the values you could use. It's all going to be fairly arbitraty, but it's good not to make the 5 micrometer cilia worth as much as the 50 micrometer flagella for example. By the way, sizes, would those be interesting as well?
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PostSubject: Re: Microbial Compounds and Organelles   Mon Jan 14, 2013 5:43 pm

Sizes only matter for graphics and to determine whether everything you tried to squeeze into the cell really fits. As the second one is alredy limited by the same thing that limits maximum size of a cell, I would say that sizes are important, but we can skip them for now (unless there is something i'm missing).

We know thermoplasts dont exist in nature (at least as we imagine them). Probably it is because it's not efficient and nature discarded it. Maybe nature never tried them. We would like to add them, for completionist's sake, even if the reactions they simulate are not really possible.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 1:58 am

@Previous Page of posts: So the propulsion equations are all we need then? No collision mechanics?
Also, which variables do flagellum and cilia tweak in the equations to increase or decrease speed/acceleration?
Once we get this done I'll compile it all together and add it all as the next step for the "Building Microbe Stage" thread.

@New Page of posts: Wow, great to see you are so knowledgeable on the subject Toughtopay. Most of what you and the others discussed is wonderful and I will have a more in depth look of tomorrow, but bear in mind not to go too in depth with the realism. At the end of the day, it's still just a video game.

@Seregon: Thanks for the format for the organelle listing, that looks much clearer and concise then what I was using. I will try to get some more organelles added to the list I made earlier, then I'll repost it, and then you guys can contribute and correct.

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 3:08 am

Colision mechanics are still needed. I'll try to look for formulas for them.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 8:19 am

Daniferrito wrote:
Colision mechanics are still needed. I'll try to look for formulas for them.

Colisions between object are basicly govrend by the normal laws of classical mechanics.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 10:44 am

Yes, but that doesent mean that the formulas are easy. I've found that wikipedia (here and here) has some formulas for them. They are inclomplete for 2 dimensional colisions, but those formulas are a start.

Edit: I believe a better rephrasing of what i said would be that even through the formulas are basic physics, we still need to have them.


Last edited by Daniferrito on Tue Jan 15, 2013 5:09 pm; edited 1 time in total
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 12:14 pm

Daniferrito wrote:
Yes, but that doesent mean that the formulas are easy. I've found that wikipedia (here and here) has some formulas for them. They are inclomplete for 2 dimensional colisions, but those formulas are a start.

We shoulden't use Elastic collisions as we arn't modeling gas or particales.

Also, this is getting too accurate, And will require to use ODE's (For exemple http://en.wikipedia.org/wiki/Tsiolkovsky_rocket_equation#Derivation ) and other equations or as wikipedia says: "The algebra involved can be cumbersome" we arn't here for a physical simulation... Please note that the elastic equation in the Inelastic collition are in one D (There is x, y and y = f(x)), if we are going to do this in more d's it might involve PDE's (DUN DUN DUN...).

As a dude that tried (And is trying) to solve the simplest heat equation (PDE) and Simple ODE's, I tell you, these equations are VERY hard.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 12:30 pm

Neither ODE's nor PDE's would be a problem to simulate, please don't make them sound scarier than they are. Remember that we're not trying to 'solve' anything (in the mathematical sense), but to simulate a system - the question is how accurate we want to be.

Knowing the differential equations involved would be a good start, and we could build a simple system by tracking (all variables below are vectors with x and y components):

Position p at time t.
Velocity v = dp/dt
Acceleration a = dv/dt

Each timestep (frame) we can then calculate p(t) = p(t-1) + dt * v(t-1), v(t) = v(t-1) + dt * a(t-1). a(t) will probably be a fairly simple function of mass and drag (unless we want to model inertia too, in which case n = da/dt), such as those Dani mentioned.

To model a collision, we note the mass and velocity of each body before the impact (t), and then modify v(t+1) to take into account the velocity transfered in the collision (less the energy lost to inelasticity). I'm no physicist, so I don't have those equations in my head, but I've seen them before and if need be I'm sure I could look them up again.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 1:09 pm

Seregon wrote:
Neither ODE's nor PDE's would be a problem to simulate, please don't make them sound scarier than they are. Remember that we're not trying to 'solve' anything (in the mathematical sense), but to simulate a system - the question is how accurate we want to be.

Knowing the differential equations involved would be a good start, and we could build a simple system by tracking (all variables below are vectors with x and y components):

Position p at time t.
Velocity v = dp/dt
Acceleration a = dv/dt

Each timestep (frame) we can then calculate p(t) = p(t-1) + dt * v(t-1), v(t) = v(t-1) + dt * a(t-1). a(t) will probably be a fairly simple function of mass and drag (unless we want to model inertia too, in which case n = da/dt), such as those Dani mentioned.

To model a collision, we note the mass and velocity of each body before the impact (t), and then modify v(t+1) to take into account the velocity transfered in the collision (less the energy lost to inelasticity). I'm no physicist, so I don't have those equations in my head, but I've seen them before and if need be I'm sure I could look them up again.

Well, if you have a way to simualte them in an effcient manner and not solve them many times, you are welcome... Anywho my suggestion is to model Perfect inelasticity to reduce resurce use, I am also not sure how much inertia would effect the player so we need to consider ignoring it.

I used extreme descriptions to make a point: While we don't want to make an unrealistic game, we diden't come here to create the SuperDuperUberBBQ Scientific simulation... Making models and concept is fun, but after all, we do want some results in a normal time - frame.

Now, how are we going to deal with space - time carvarture and the EFEs in space stage?
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 5:08 pm

If you try to solve the equations on paper, or even worse, try do do derivatives or integrals (i hope i didnt write those words the wrong way), these equation are going to be realy bad.

If you try to get the element number n of the series of fibonacci, without needing to calculate firstly n-1 and n-2, you will pass your entire life thinking about the solution, and you probably will never find it. On a computer, you can just tell it to calculate each element of the series, and you will finish much faster.

About the rocket formula, here it is:
Spoiler:
 

Anyway, we definetly need colisions. Else the cells would float throu each other, as ghosts.
I believe we are getting too off-topic. This thread is supossed to be about organelles.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 7:28 pm

Okay, then take the collision discussion to the "Building Microbe Stage" thread. We'll keep this open for further organelle stuff later on.

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 7:59 pm

So Toughtopay what are the significant differences between flagella and cilia?

Also, in the equations we had earlier, which variables would flagella and cilia affect to increase the max speed or acceleration of a cell?

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 8:14 pm

Alright, if anyone has the heart to read my very largely incomplete organelle table, I have it hosted on google docs, here is a link (used to be a link).
In addition to the table I explained my current process so that, if anyone has a better idea or believes some of those steps are unnecessary they have a chance to let me know and I can be all the more productive.

And here's my pathetic start at making a list of compounds (used to be a link). I'm too tired to do anything more elaborate today. I think this is fair progress though. I have a friend visiting me on Thursday from a foreign country. He'll be staying a week, so I won't get much (if anything) done during that period. If anyone volunteers to do my part of the work I'll gladly exchange pms to discuss what I've been doing so they don't have to start from scratch.

I'm still planning on making some progress until then though.

EDIT: I'm not allowed to post links for another couple days. I don't care. Any idea how I can get around this?

Also cilia are 5 to 10 micrometers long, while (eukaryotic) flagella are >=50 micrometers long. Cilia sort of just flail around to generate movement, while flagella have a very sinusoidal movement. They're the same structurally, but on different scales, and because of that the movements are different. The cilia simply isn't long enough to have a sinusoidal movement, but it's short enough for some weird physics energy efficiency by using its momentum. I'm incapable of explaining it. In short, flagella consume more energy but offer more speed, while cilia consume less (even if, when combined, they would form a similar flagella) but also offer less speed.

As for the variables you could attach, I would say that as long as you have sufficient ATP there isn't much you can change. Oh, you could have a less rigid cell membrane. But that's about it, unless if you're planning to have more or less viscous environments, but I'm assuming this would be unnecessarily complicated. Or the question wasn't even posed to me, I just realised you referred to previous equations which you probably (and rightfully) assume I'm not familiar with.
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 8:23 pm

For links, you can just leave out the www. or the .com and point that out.

I'll let one of the more advanced physicists answer the question on which variables propulsion organelles (aka flagella and cilia) increase, as I don't have sufficient knowledge on the topic.

Great work though. I'm interested to see the links.

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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 8:29 pm

https:/Xdocs.googleY/folder/d/0B6c9x8zUW_2saWJXNHJzdUtrOXM/edit
This links to the folder where you'll find both files, their names are pretty straightforward. The X is a "/" and the Y after "docs.google" is a ".com"
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PostSubject: Re: Microbial Compounds and Organelles   Tue Jan 15, 2013 9:01 pm

Wow, awesome work. Unfortunately, this is far beyond my level of understanding of biology, or sciences in general, so again i will have to let the discussion carry on with the others, but nonetheless great work.

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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 16, 2013 8:18 am

Daniferrito wrote:
If you try to solve the equations on paper, or even worse, try do do derivatives or integrals (i hope i didnt write those words the wrong way), these equation are going to be realy bad.

If you try to get the element number n of the series of fibonacci, without needing to calculate firstly n-1 and n-2, you will pass your entire life thinking about the solution, and you probably will never find it. On a computer, you can just tell it to calculate each element of the series, and you will finish much faster.

About the rocket formula, here it is:
Spoiler:
 

Anyway, we definetly need colisions. Else the cells would float throu each other, as ghosts.
I believe we are getting too off-topic. This thread is supossed to be about organelles.

I believe I know what confused me, I thought that you were trying to simulate it "Perfectly" I mean, to simulate all of the PDE/ODE like chaotic (The Chaos theory sense of the word) and "Super" dynamical behavior.

Also I diden't ment that we don't need any colision, but we don't the most realistic one.

P.S.
There is more than one version of that model, right?

But that defently not an ODE.
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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 16, 2013 8:29 am

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.
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Toughtopay
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PostSubject: Re: Microbial Compounds and Organelles   Wed Jan 16, 2013 8:36 am

I only personally added three or four things, if we ignore the part where I detail the membrane. That part is mostly just for me while I figure out how to group things together to make something simple.

Everything other organelle is from the threads, I just began adding what they're made out of (compounds which won't need to make sense to anyone, just be used as resources) and from what I read so far people there are some really savvy people here. Phospholipids were mentioned before I even got here for example. Don't get me wrong I'll still try to simplify and make it more intuitive, but I don't think I'll be able to do that to an important extent.
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PostSubject: Re: Microbial Compounds and Organelles   Today at 10:04 pm

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Microbial Compounds and Organelles
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