Studies of Cell Lab - Volume I

Here anything Cell Lab related that doesn't fit into the other topics can be discussed.
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Nayus
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Studies of Cell Lab - Volume I

Post by Nayus » Wed Jan 04, 2017 9:42 pm

I've been working on these since I finished the Drone Ant Queen :lol: and it's why I couldn't make any more organisms or Challenges.
>It came to me that, other than the general explanations in the game and some explanation here, we didn't know much about the working or the laws of the game. So I proposed to myself to tackle some of this issues. I did some experimentation and used the recolected data to get to conclutions on how exactly the CL Universe works.
>Now, I know that most of the things I came to realize here would have been much more easily found by looking at the code of the game... but that wouldn't have been that fun. As a future researcher (?, I can't look at the code of reality, so this is like a test or little tease in what I would be doing in a couple of years. :lol:
>Okay sorry for all the useless introduction. Here it is the Random Experiments and its Conclutions.


First of all I'll give just the conclutions I got, instead of all the process. So then I'll write the experiments with detail.
Random Cell Lab Experiments
Vol. I
Just the conclusions:
  • -Every cell lives exactly 240h
    ---Cells affected by a Virocyte don’t reset its Cell Age
    ---Stemocytes that change to another mode don’t reset it Cell Age
    ---No other action performed by cells change its life span
    -Every cell that is placed from the Genome Editor into the microscope spawns with a mass of 3ng
    ----*Lipocytes placed could spawn with more mass (but it's not very likely).
    -Cells don’t spend the same amount of energy, here in order of higher consumption to lower:
    --Photocyte
    --Virocyte
    --Flagellocyte, Devorocyte, Phagocyte
    --Flagellocytes spend more energy when moving
    --Secrocyte
    ----*Secrocytes don't change its consumption by changing any of the substances it can produce.
    --Nitrocyte, Myocyte, Neurocyte, Buoyocyte, Stemocyte
    ----*Myocytes spend a bit more energy if they are bending, lifting or contracting
    --Glueocyte, Stereocyte, Keratinocyte, Senseocyte
    --Lipocyte
    ----*Lipocytes spend almost noenergy (Could be directly 0)
    -Salinity does not affect the way nutrient chunks in the substrate degrade and disappear.
    -Salinity affects the way Cell consume its nutrients in a Quadratic form.

    -Every cell dies when it has 0.6ng of mass or lower (not completely prooven)
    -Smaller Cells spend more energy than bigger ones of the same Mode and Type (hypothesis)
Cell Age

Just put any cell in system that would let them live indefinitely but not reproduce and you’ll get the same result. Every cell lives 240h. Exactly 10 days. There’s no differentiation in cell type or anything. This was, honestly, a surprise for me because in some Challenges and experiments it seemed like some cells were immortal and others not or maybe that they have huge difference in age spans. Sometimes half an organism will die while some cells will live. The reality is quite simpler in this regard. They just look like they don’t die but in every case they are just reproducing. Daughters will have cero age, even if they have the same function or replace the mother, and just keep the work they had in the organism. So, in Theory, we could make an organism that doesn't die of age by way of spliting it to itself and a game of turns in higher nutrient priority. No need for the Phoenix or Stemocyte route I've been using ...That's an idea to add to the bank list.

One thing to notice is that Stemocytes that change in other modes maintain the original Stemocyte age, so they aren’t a cell becoming another, but instead one cell just changing its mode.
The same thing happens with cells that have been affected by a Virocyte. They change modes but they don’t reset its age.
Other than that, no particular function of any cell lowers or alters in any way the amount of time it can live.


Consideration in Time Measurements

Several of the experiments done here needed lots of time measurements, and in some of them accuracy was a key factor, but in the early experiments I saw something quite particular in how the screen shows how things happen. If I place a cell with minimum split mass, the changes go like this:


Image

The screen showed the change at 0.4h, not 0.5h.
Also in the Cell Age experiment, it changed in the 239.9h, beginning the 240h with the change already in place. However, I don’t think Petter would just say cells split with a minimum 0.5h age and actually set it to be 0.4h. So, with this as a start point, it made way more sense if the number were actually 0.5h and 240h respectively. I concluded that a change doesn’t take place in the exact time the measurement screen changes, but instead 0.1h later. It isn’t a matter of calculations or a bug, I think, but just how the game shows the changes. With this in mind is how I did all the time measurements.

First Measurements

I started with a simple experiment. I put one of every cell in a frozen substrate with a specific salinity and then touched Observe and wrote down when the cell died. At first, I did only two measurements with different salinities and systems. But with the numbers that came out and the trouble I had later trying to figure out something of consistency, it became clear that I had to do more. Here are the results

The salinity was one of the big issues. It wasn’t as straightforward as I thought it was. I ended up using the measurements were salinity is 0.000 because I simply don’t understand how it works. However, I leave here the other measurements anyway:

Image
Image

Even though in the actual numbers it isn’t clear yet the connection to salinity or actual proportions, I can now propose a new classification for the cells, based in their Energy Consumption:

[quote]-Low Consumption: Glueocyte – Stereocyte – Keratinocyte – Senseocyte
-Medium Consumption: Secrocyte – Nitrocyte – Myocyte – Neurocyte – Buoyocyte – Stemocyte
-High Consumption: Phagocyte – Devorocyte – Flagellocyte – Virocyte – Photocyte
[/quote]

With the Virocyte and Photocyte being quite high compared to the rest. The fourth category is the no consumption. Currently, the Lipocyte is the only cell in this category.
  • It should be said that Lipocytes could spend energy (measurements aren’t exact enough to confirm this), but it is so low that alone in any substrate, it dies of age, never of starvation. So it’s trivial.
I think this would give us an advantage when creating new organisms. If we were in a position when we don’t know what cell to put there if we have two options, this classification would help.

Spawn Mass

When we put cells in the microscope they don’t spawn with the max 3.6ng possible mass. Neither they spawn very small. For the sake of measurements and further calculations, I needed to know what was the exact mass any given cell has in the instant that we place it from the Genome Editor. When I did the first measurements, I didn’t thought the salinity would play a part that wasn’t just obvious in the results. It turns out Salinity affects how cells consume its energy in a Quadratic form that I can’t calculate yet because I don’t have the mathematical knowledge yet. So the calculations I ended up using were with Salinity: 0.000
Anyway, here’s what I did in every case: I put in the Microscope a cell with a certain random Split Mass and see if it split. If it did, I’d increase the Split Mass, if not, I’ll decrease it. So I’d go back and forth until I got to the limit. This limit means that the first value is the maximum Split mass that the genome can have and the cell will split, and the second value is the minimum Split mass so it won’t split.


Image

The difference between different cells is expected, because every cell needs to be 0.5h old to be able to split, and in that time, it spends energy. Therefore, cells with a high consumption would need a lower split mass to be able to split, because they spent more energy before that 0.5 mark.
The experiments with Lipocytes indicate a Split Limit of [2.99ng~3.00ng]. And since it does not spend an appreciable amount of energy, but not 0, I concluded that the Spawn Mass must be 3ng.
  • It might be that Lipocytes placed in the Microscope have a higher mass to begin with, or maybe that every cell has a different spawn mass (which throws away all my conclusions in a second but I have a strong feeling that it isn’t the case). I’ll take as a start point that the cells do have the same spawn mass and see if my conclusions check out backwards with the data later on.


If I’m right, then any given cell placed from the Genome Editor spawns with a 3ng mass, low consumption cells use ~0.14ng (in 0.000 salinity) in the 0.5h that takes the cell to split, while Photocytes, for example, use ~0.605ng in that 0.5h.

Nutrient Remains

Before the next topic, which is a big one, I have to discuss this. I realize this way too late and I had done many calculations and measurements to this point that would become useless ‘cause I didn’t remember that cells leave some nutrients when they die. This probably meant that cells didn’t die when they have 0.0ng of mass, but instead they reach a certain mass that is so low that kills the cell. It was a show of a considerable short sight on my behalf, but whatever… I could fix it.

The first thing that I did was to see if Salinity (which was already giving me a headache) affected the rate at which the nutrient remains, or chunks, lose mass and disappear. The good news is that it doesn’t. A Photocyte in a 0.000 salinity substrate left a food chunk that lasted ~10.5h after the cell died, just as much as the same left chunk in a 1.000 Salinity. Also just as much as a chunk left by a Phagocyte in both 0.000 and 1.000 Salinity. So they all decrease at the same rate, no matter what Substrate they’re in.
And since the remains of a Photocyte and the ones of a Phagocyte lasted the same, I conclude that all cells die when they reach the same minimum mass and (maybe or) leave the same remain.

Now to calculate what is this minimum mass any cell can have to live, I have to assume two things I can’t really prove:

1) That the mass that the cell has the instant of its death by starvation is exactly the same mass as the nutrient chunk left by this cell.
2) The Phagocyte that eats any nutrient chunk takes its mass completely, with no loss.


Maybe there’s a way to test these things, that I can’t see, but anyway I’ll have to work with this assumptions. I made another experiment that gave the number:
I put a Photocyte in a Substrate with no energy source of any kind and carefully waited until the instant it died, exactly then I froze the Substrate and placed a Phagocyte exactly on the left chunk with a determined Split Mass.
I already know the Split Limit of the Phagocyte, [2.67ng-2.68ng] at salinity 0.000 and [2.86ng-2.87ng] at salinity 1.000. Now if I place this Phagocyte on the left chunk, it gains some mass, therefore the Split Limit will rise exactly how much mass it gained. With this and a similar experiment as the one that gave me the Split Limit to begin with, I obtained the same value with salinity 0.000 and Salinity 1.000: 0.6ng. This number is, then, how much mass a cell leaves unused when it dies. Again, only if the two of my assumptions are correct


Cell Energy Consumption

Not all cells spend the same amount of nutrients to subsist. We all know this; however, here’s a closer examination in how this works and what the ranks are.

First: Some cells have some notes that are worthy of pointing out:
-Myocytes will spend a little more energy if they are bending, stretching or lifting
-Secrocytes spend the same amount of energy, no matter what substante it’s producing

I’ll use something I call the Index of Consumption to describe how much any cell uses in energy. This index and the calculations use every topic described before.
The unit it works in (for now) is ng/h (how much ng spends in one hour). I would have created a unit but I think that would be kinda arrogant for my part.
Until I figure out how salinity play is in this, the index is expressed in the form

Ic = m/t
Where m is the mass of the cell that is consumed, and t is the time that takes to consume it.
Each cell has its own Ic, but it also depends of the Salinity… in a form I don’t quite get yet. So technically for now the Ic=m/t is just while salinity = 0.000

Taking the spawn mass and the time that each cells survives, the results are the next.
(I’ll leave two tables. The first one is with the corrections made for the Nutrient Loss that the cell has when it dies, the second one is the original calculations I obtained.)

Image

There’s the problem of accuracy now.
For example, my cellphone says that the Photocyte cell with 0.000 salinity and no food dies at 2.8h. If I apply the formula Ic = m/t I get an Ic of:
Ic= (3ng-0.6ng)/2.8= 6/7 = 0.8571
But if the simulation missed the time just by 0.1, meaning it was for example 2.9h, the result becomes
Ic= (3ng-0.6)/2.9 = 24/29 = 0.8275

It’s an error of 0.029. At first glance, it doesn’t seem like much, but then I try to circle back to the data:

I got before that the Limit Mass of a Photocyte in 0.000 salinity is [2.39-2.40], meaning that a Photocyte spends 3 – [2.4~2.39] = [0.6ng~0.61ng] in 0.5h. If I multiply by 2 so I should get the supposed index, but I get [1.2~1.22]
Not a margin of 0.029 anymore, but 0.3628 with the supposed “corrected” measurements. With the incorrect, I get a difference of 0.1088.
That’s the worst thing, because I’m now led to believe that the corrections with the chunk of mass dropped by the cells are wrong. They get me away from the other measurements, instead of closer.
So the difference gets to a point I have to doubt if my measurements or methods are right. I mean… It’s not much, really I decided I’d use all Ic in every case and see which one gave consistent results.

Here’s the third Ic calculation. Like I said this one was calculated like this: I’d take the Split limit of any cell and subtract it to 3. This would give me the amount of mass the cell consumed in a 0.5h period. Then I’d just multiply it by 2 so I’d get the Ic.


Image

A comparison:


Image

Image
thanks to bwisialo for the tip in graphs


NOTE: This graph is worthy of analisis: The green and yellow lines (the Ic calculated with starvation death in mind and Ic calculated with Split Limit) produce the same proportions (the lines appear to be parallel) but with an interesting chunk of difference. This tells me that the calculations of the nutrient loss by death are right, or at least consistent with the proportions made with the Ic calculated by Split Limit, but both differ quite notoriously.
The calculations of Ic by Split limit are definetly wrong. If they were right, that'd mean a Stereocyte placed in a 0.000 salinity Substrate would have to spawn with 20.02ng of mass in order to survive the 71.5h it currently survives. So there's definetly some number wrong in the Ic by Split Limit. In these calculations by Split Limit only one factor is exactly equal in all the Cells, and that is the Spawn Mass of 3ng. That leads me to believe that maybe I am wrong with the 3ng number, or at least that at first glance that cells don't spend its energy as directly as I thought (an hypotesis that in a moment will have another proof).
The closer we are to the correct Ic, I think, are the Ic calculated with the nutrient loss by death table.


Mass Loss
One thing I wanted to figure out and I think is important is to see if there’s mass loss when cell reproduce. I devised two different methods to find out this but both depended in something quite important that screw everything up :cry:

I did this experiment. In a substrate with Light Range at max, a certain Light Amount and 0.000 Salinity. I placed a Photocyte with a high split mass. I wanted to know exactly the amount of light that made Photocyte neither grow nor die. The exact point when the cell stays its size.
Sadly at 0.47 of Light amount occurred something particular. The cell grew enough to split, but its daughters started to lose mass, instead of gaining it. Both were Photocytes, both even the same Mode in the genome.
I was baffled. This means that… at least the Photocyte, acquires energy depending on its size. Smaller cells spend more energy than the same mode and type of cell but bigger.

I don’t know… This could throw to the trash almost everything I concluded related to Nutrition Consumption… It could also explain a lot of behaviors I couldn’t explain yet but anyway. I think it’s enough for Volume one. Maybe in Volume Two I could give some light to the issue, as well as the so annoying Salinity problem (also the difference of Nutrient Consumption in the different speeds of the Flagellocytes I skipped here)

I hope some of the conclusions or information in this help somebody in some way. Tell me please if you find some mistake or have some doubts in the way I approached the experiments... or anything. :D Good day
Last edited by Nayus on Thu Jan 05, 2017 7:20 pm, edited 1 time in total.
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wapcaplet
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Re: Studies of Cell Lab - Volume I

Post by wapcaplet » Thu Jan 05, 2017 5:24 am

Wow, awesome analysis! I have often wondered about initial cell mass, and the differences in energy consumption between cell types, and I agree that doing experiments to learn these things is more in the spirit of the game than just asking Petter what's in the source code. I will definitely be reading this post several times. Thanks for sharing your findings.
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Re: Studies of Cell Lab - Volume I

Post by bwisialo » Thu Jan 05, 2017 7:58 pm

Wow, full scale dork-dom! :D You deserve a :ugeek:
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Re: Studies of Cell Lab - Volume I

Post by wapcaplet » Fri Jan 06, 2017 1:18 am

Here's a small contribution to the salinity problem:
cell-lifespan.png
The Y-axis is life span in hours, and the X-axis is salinity. Click/tap for a larger image if this one is too hard to read.

I got the same numbers as you Nayus (or close enough) for 0.0 salinity, and I chose only one cell from each of the groups you listed (under the assumption that the others in the same group will have the same curves).

I am not sure what mathematical curve these are, but clearly life span increases more rapidly as you get closer to 1.0 salinity. Lipocytes have maximum 240h lifespan regardless of salinity. Gluocytes reach maximum lifespan somewhere just below 0.8 salinity. The Nitrocyte and Secrocyte reach maximum lifespan somewhere between 0.9 and 1.0 salinity, but their curves are a bit off at the top since I only tested 0.9, 0.95, and 1.0. Phagocytes, Virocytes and Photocytes won't last more than 100h without an energy source, and last substantially less than 100h if salinity is not at maximum.

Some relationships seem to hold across all salinity levels (except beyond the 240-hour maximum). For example:
  • Gluocyte ~= 2 * Nitrocyte
  • Nitrocyte ~= 5 * Phagocyte
  • Phagocyte ~= 2 * Virocyte
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Re: Studies of Cell Lab - Volume I

Post by Nayus » Fri Jan 06, 2017 6:44 pm

I got a similar result so we're on the right track! Thank you webcablet, that data will go right in the reasearch! :) :D
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Re: Studies of Cell Lab - Volume I

Post by Nayus » Fri Jan 06, 2017 11:31 pm

@wepcaplet Am I seeing this wrong or in the curves (mainly the Nitrocyte and Secrocyte ones) appears to be some kind of decreasing in the curve in the higher Salinities?
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Re: Studies of Cell Lab - Volume I

Post by Reaper Elite » Fri Jan 06, 2017 11:35 pm

I see it too, kinda contradictory to the trend.
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Re: Studies of Cell Lab - Volume I

Post by wapcaplet » Sat Jan 07, 2017 4:38 am

Nayus wrote:Am I seeing this wrong or in the curves (mainly the Nitrocyte and Secrocyte ones) appears to be some kind of decreasing in the curve in the higher Salinities?
That's what I meant about the curves being off. I'm pretty certain it's an artifact of the limited data points I chose. For example the gluocyte probably maxes out somewhere between 0.7 and 0.8 salinity, but I didn't test at 0.75 or other intermediate points. Similarly, the nitrocyte must hit maximum between 0.9 and 0.95, and secrocyte between 0.95 and 1.0. Doing more sampling in those ranges (say, at 0.925 and 0.975 salinity) would surely yield a better looking graph. :geek:
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Re: Studies of Cell Lab - Volume I

Post by bwisialo » Tue Jan 10, 2017 12:01 pm

A whilw back Petter posted a list, from the source code, on how much energy each cell ype uses.

viewtopic.php?f=5&t=1569&p=8527
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Re: Studies of Cell Lab - Volume I

Post by bwisialo » Tue Jan 10, 2017 12:02 pm

A whilw back Petter posted a list, from the source code, on how much energy each cell ype uses.

viewtopic.php?f=5&t=1569&p=8527
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