Easy Evolution

Post your own challenge to your fellow researchers!
CannedGoods
Posts: 28
Joined: Mon Mar 06, 2017 1:18 am

Re: Easy Evolution

Post by CannedGoods » Sat Dec 07, 2019 8:05 am

An interesting experiment result using the challenge substrate, contamination and radiation only. A very interesting mix of cells in the genome, although, in retrospect, I don't think I actually fulfilled any of the mentioned challenge goals. :cry:

Substrate: https://www.dropbox.com/s/vnvitf7tebbv3 ... trate?dl=0

Image

Mainly this is an exercise in my re-learning how to document and share my experiments AND to turn my skills with Splunk (FREE data analytics software) against this simulation data.

Image
  • Top chart is the birth and death rate relative to available food.
  • Middle chart is the total number of cells by color-group (WARNING: Graph color in Splunk does NOT correspond to Cell Lab game color).
    NOTE: Top and Middle chart scales are logarithmic progression (1, 10, 100, etc.) not linear (1, 2, 3, etc.)
  • Bottom chart is the percentage of the total number of cells by color-group.
All I have to do is type the CSV name corresponding to the experiment I want to chart into the box at the top, "Experiment to Chart," and viol la! I'm sure I can find other interesting things to pull out of this, but I wanted to share what I came up with so far because it looks so cool! One can see extinction events, the genome evolve over time, more efficient and stable, as you showed in your chart.

Speaking of efficiency... I can have Splunk express the efficiency of the ecosystem as a single ratio, by dividing the number of births (splits) by the available food mass. More experiments!
Last edited by CannedGoods on Fri Dec 13, 2019 10:17 pm, edited 1 time in total.
CannedGoods
Posts: 28
Joined: Mon Mar 06, 2017 1:18 am

Re: Easy Evolution

Post by CannedGoods » Thu Dec 12, 2019 6:48 pm

Gene Pool = Phagocyte, Flagellocyte ,Photocyte, Buoyocyte, Gleocyte and Ciliocyte
Radiation level = 0.003 or 0.000

This Gene Pool and radiation level got me to achieve "Hard objective: Ecosystem niches" with 2 and 3 cells in relatively short order several times. At 14,700h (14.7kh) there are 2 genomes coexisting. 3 coexisting at 19,500h (19.5kh).

(o) Samples (o)
ImageImageImage
1.8kh (o) https://www.dropbox.com/s/74n9jlgbc0bb2 ... trate?dl=0 | 8.8kh (o) https://www.dropbox.com/s/ri6mjixms6eod ... trate?dl=0 | 10.5kh (o) https://www.dropbox.com/s/sne32jem0sagb ... trate?dl=0
ImageImageImage
14.7kh (o) https://www.dropbox.com/s/c2spduybay9d7 ... trate?dl=0 | 18.4kh (o) https://www.dropbox.com/s/mi0l02d4k2nj5 ... trate?dl=0 | 19.5kh (o) https://www.dropbox.com/s/o3ao0plnqno3x ... trate?dl=0
Image

In the abundance of light, the photocytes dominate this ecosystem. They are prodigious reproducers and connected by a mycelium-like network of adhesin that distributes the intense light energy from the fringes of the substrate plate, at the expense of culling some it's youngest buds on the edge. As the photocytes expand relentlessly, the eldest cells get pushed toward the bottom of the substrate, further and further from the light. As the supply lines of adhesin grow longer, so do the number of cells feed from that energy, until finally the cells in the depths of the sample, start to become starved, shrink and die near the region of the density gradient.

It is there, near the density gradient, that the 2nd genome of phagocytes thrives on the food pellets left behind when the photocytes starve to death. They whole colony lives slightly below the density gradient and is perpetually falling upward in a wedge formation. When the crescent of dusk no longer provides enough light to the photocytes the phagocytes are ready to sweep in and gorge themselves. In this particular evolution, a buoyocyte adaptation allows the phagocytes of this genome to probe the photocyte colony under which stockpiles of unused food mass energy sit.

In the small niche remaining at the bottom of the substrate one will find the 3rd and final genome; A genome buyo-phages sparkle in the depths, nibbling at the bits of food energy it can find spawning in the dark depths of the substrate.

About the Data
The sample at 18.4kh (18,400h) was frozen at the moment the 3rd genome (the photocyte) evolved and bull-dozed it’s way across the top-half of the substrate, and also at the leading edge of where the population maxes-out the substrate limitations. The ecosystem is very robust and “fit” if one defines such by the Cell Count, the maximum of which may be no more than 1,000 cells, per the substrate advanced settings.

Data Logging was set to every 5h, however, for Splunk, there is a limitation of 10,000 data points to be displayed in chart visualization. To accommodate this limitation, I told Splunk to put Time into Bins that are 10h in size, then give me the Sum of each cell color-group within each 10h period and chart THAT instead. So… that means a Sum of 2,000 cells means there were 1,000 cells on the plate for two consecutive log events. In retrospect, it would be less confusing to chart the Average instead of the Sum, and I already updated the chart to display Average instead going forward.

About the Splunk Dashboard
I’m making revisions to my Cell Lab dashboard in Splunk, daily at this point. I would like to share this work with the community. I will make a separate forum thread where I can share my Splunk Dashboard with the community. You would need to install Splunk, setup the “cell-lab” Index (easy), and then put some Cell Lab “statsX.csv” data into said Index (also easy). Then, all you would need to do is start a blank dashboard, go into Edit mode and paste in source code from my dashboard, and then you may have my dashboard too!
Last edited by CannedGoods on Sat Dec 14, 2019 5:23 am, edited 8 times in total.
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WhatTheSillyName
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Re: Easy Evolution

Post by WhatTheSillyName » Thu Dec 12, 2019 6:52 pm

CannedGoods wrote:
Thu Dec 12, 2019 6:48 pm
At 14,700h there are 2 genomes coexisting. 3 coexisting at 19,500h.
I'll edit post to add substrate links and more text later.
Umm... All images are unavailable. Is this my problem?
CannedGoods
Posts: 28
Joined: Mon Mar 06, 2017 1:18 am

Re: Easy Evolution

Post by CannedGoods » Thu Dec 12, 2019 7:45 pm

WhatTheSillyName wrote:
Thu Dec 12, 2019 6:52 pm
CannedGoods wrote:
Thu Dec 12, 2019 6:48 pm
At 14,700h there are 2 genomes coexisting. 3 coexisting at 19,500h.
I'll edit post to add substrate links and more text later.
Umm... All images are unavailable. Is this my problem?
I see images using Chrome, but unavailable in Internet Explorer. I'm probably doing something wrong. Using the wrong shared links from DropBox or something.

EDIT:
Dropbox wants to hold your files hostage.
https://www.dropboxforum.com/t5/Files-f ... d-p/211678
Reply that says "dl.dropboxusercontent.com trick broke on March 15, 2017 1:32 EST," is not correct and this trick DOES currently work now.

EXAMPLE: Current link
https://www.dropbox.com/s/kwyt8v55bhbj3 ... e.png?dl=0
WORK AROUND:
https://dl.dropboxusercontent.com/s/kwy ... e-blue.png
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WhatTheSillyName
Posts: 231
Joined: Thu Aug 03, 2017 2:13 pm
Location: Hong Kong
Contact:

Re: Easy Evolution

Post by WhatTheSillyName » Fri Dec 13, 2019 9:29 am

CannedGoods wrote:
Thu Dec 12, 2019 7:45 pm
I see images using Chrome, but unavailable in Internet Explorer. I'm probably doing something wrong. Using the wrong shared links from DropBox or something.

EDIT:
Dropbox wants to hold your files hostage.
https://www.dropboxforum.com/t5/Files-f ... d-p/211678
Reply that says "dl.dropboxusercontent.com trick broke on March 15, 2017 1:32 EST," is not correct and this trick DOES currently work now.

EXAMPLE: Current link
https://www.dropbox.com/s/kwyt8v55bhbj3 ... e.png?dl=0
WORK AROUND:
https://dl.dropboxusercontent.com/s/kwy ... e-blue.png
Wow, it works.
Visualizing the data is very good to see.
And thank you for mentioning the software.
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