Cultivating Coexistence – “Chaos” Substrate

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Nayus
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by Nayus » Sat Mar 11, 2017 2:20 am

This raises a potentially interesting question. Where exactly is the line where you call 2 genomes, different organisms? In what aspects you define difference and relation between Genomes?

I got to the "Hard" part of the challenge, though
Last edited by Nayus on Sat Mar 11, 2017 3:33 am, edited 1 time in total.
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bwisialo
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by bwisialo » Sat Mar 11, 2017 3:31 am

There are some loopholes to this, but I'd start with this. Two organisms: each of the two has a closed reproductive cycle such that neither produces the other. Technically, you could have one genome produce two organisms. Any two genomes that are not identical would be two genomes.

Edit: I used "organisms" to mean "species," but you coild also use organism to mean an individual member of a species, depending on what sort of species you have.
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by CannedGoods » Sat Mar 11, 2017 7:22 am

bwisialo wrote:There are some loopholes to this, but I'd start with this. Two organisms: each of the two has a closed reproductive cycle such that neither produces the other. Technically, you could have one genome produce two organisms. Any two genomes that are not identical would be two genomes.

Edit: I used "organisms" to mean "species," but you coild also use organism to mean an individual member of a species, depending on what sort of species you have.
That's a good start. I like that.

Is it more or less clear if we say it like this?
Two species of genomes: Any two not identical organisms, each with a closed reproductive cycle, such that neither produces the other.
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bwisialo
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by bwisialo » Sat Mar 11, 2017 8:07 am

I think "species of genomes" is less clear. Alast and I have used "species" in Objectives for many of the youtube challenges, and I think we took our lead from in-app objectives. Eg, Can you create a species that reaches a cell count of x? I tend use species to mean: a group of organisms that have the same genome and reproductive cycle.

I tried some other rewordings to incorporate everything but just made things sound complicated. ;) Pinning down the wording for this challenge probably isn't necessary as long as you know what you mean and can use it consistently to determine how many species and genomes you have on the plate.

I'm guessing you saw the True Evolution Challenge. I've tried it, but by developing solutions from contaminated cells on a challenge by challenge basis, without the solutions having a common ancestor.
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Noughtypixy
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by Noughtypixy » Sat Mar 11, 2017 3:50 pm

Nayus wrote:This raises a potentially interesting question. Where exactly is the line where you call 2 genomes, different organisms? In what aspects you define difference and relation between Genomes?

I got to the "Hard" part of the challenge, though
I have been spotting for an organism that only reproduces more of itself then copying it to look at genome then setting 1 as initial and comparing the first splits with the same from an organism I think is different to see if it actually is or is just a different section of the genome.

Thought I had 4 but only these 2 made the final cut phagodippers and duophotes
https://www.dropbox.com/s/1am6plaxe5ap3 ... trate?dl=0


Image

this little beauty is the photoworm (didn't quite make the cut) and some of its eggs
https://www.dropbox.com/s/hglvcjzmj3w79 ... enome?dl=0

Image
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bwisialo
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by bwisialo » Sat Mar 11, 2017 5:29 pm

@Noughtypixy -- What device are you using? The screen looks huge.
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by Noughtypixy » Sat Mar 11, 2017 7:48 pm

bwisialo wrote:@Noughtypixy -- What device are you using? The screen looks huge.
ASUS zenpad10
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wapcaplet
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by wapcaplet » Sun Mar 12, 2017 12:53 pm

First, I may have bent the rules of this challenge. I am using "Contaminate with random cells" at liberty, to introduce completely new genomes into the substrate when other genome(s) are already living there. This breaks the restriction on only using it in the first 100h, but my thinking is that "Contaminate" is the quickest way to get a completely new organism, rather than just a derivative of an existing genome. This hasn't helped a lot so far--if a successful genome is already living on the plate, it is very hard for some random cells to get started as a new genome that can reproduce.

Also, I have been sometimes using manually inserted cells--after evolving a genome that can self-sustain, I may sterilize and add that genome again from an initial cell. But I have not touched any genome settings; nothing was designed, it is all the result of evolution from random cells, which I think is the point of this challenge. I think I've followed it in spirit, if not the letter.

So here are some of my attempts. First, the Twin Tadpoles:

chaos-twin-tadpoles.substrate
twin-tadpoles.png
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The swimmers (green) always hatch in pairs, from a double phagocyte egg (orange). The swimmer's phagocyte head makes new double-eggs. After the head produces a double-egg, the tail flies off by itself and dies. But sometimes, very rarely, their tail will split into a devorocyte. This devorocyte, if you can believe it, also becomes an orange double-egg when it gets enough nutrients. So it's like a backup reproduction plan.

So far, they appear to survive indefinitely on this substrate, maintaining 200-300 cells.

Next, this unbelievably complicated photocyte-phagocyte organism:

chaos-elephant-man.substrate
elephant-man.png
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This thing uses, if I've counted them right, 14 modes in its life cycle, mostly phagocytes and photocytes with a sprinkling of buoycytes. The photocytes thrive in two colonies, where the light arc intersects the neutral buoyancy level. They generate phagocytes that may burst across huge areas of the plate when nutrients are plentiful. The photocyte colonies can survive on their own, and do not depend on the phagocyte portion of the life cycle--so even if some other organism eats most of the plate's nutrients, the photocyte colonies can stay alive. If either of the colonies dies, the other one can regenerate it. A later evolution of this genome has buoycytes allowing it to completely fill the top 1/3 of the plate.
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wapcaplet
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by wapcaplet » Sun Mar 12, 2017 1:55 pm

Since this is a coexistence challenge, here are two 2-species ecosystems with my above genomes. First, twin tadpoles living with a prickly parasite:

https://www.dropbox.com/s/boftzrln09m48 ... trate?dl=0
twin-tadpole-vs-prickly-parasite.png
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The parasite stays in the neutral-buoyancy band, and the tadpoles can sustain their population well in the parasite-free zone below.

Here's the elephant man coexisting with some phagocytes that make pink flagellocytes - which I call "cotton candy":

https://www.dropbox.com/s/jh8n0e2ij7ajv ... trate?dl=0
elephant-vs-cotton-candy.png
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Their flagellocyte is not attached to anything, so all it does is push the phagocytes around. The cotton candy dominates the nutrient-filled area, leaving very little for the elephant man - but the elephant man seems to do fine anyway, with just its two colonies of photocytes.
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wapcaplet
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Re: Cultivating Coexistence – “Chaos” Substrate

Post by wapcaplet » Mon Mar 13, 2017 2:00 am

One thing I love about this substrate is the way two separate colonies of photocytes can live in the neutral buoyancy band. They are like two islands of evolution, each developing and having dominant species at any given time. Even if they start with the same genome, they can diverge. Here, I placed the same purple photocyte genome in both colonies. The one on the left developed a much more complicated life cycle, with several phagocytes; the one on the right is basically a one-mode splitter. The red phagocytes making red puffs all over the place are a third genome that mutated from one of the purple photocyte colonies.
wrathful-grapes.png
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I've been starting simple--when contaminating with random cells, enable only photocytes. Hit a clean substrate with a burst of random photocytes, plus some radiation. Incubate until you have anything that will reproduce in the top left or right corners; contaminate again if they don't survive.

Once I have some photocytes reproducing, I enable other cell types--phagocytes, buoycytes, flagellocytes, maybe devorocytes. As long as some photocytes are reproducing, they can keep making new mutants that might do other things not involving photocytes.

I quite often see the double-phagocyte "peanut", like these:
three-ish-species.png
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Enabling buoycytes is a good way to get some photocytes growing at the top. But even without buoycytes, photocytes may grow all the way to the top. These, I think got pushed up by the phago-swimmers living below them. No buoycytes here, but photocytes all the way to the top:
photo-domination.png
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The green one soon took over the entire top of the plate, wiping out the brown species.

This is a fun challenge! Your substrate settings allow a lot of different models to work--the free movement provided by the density gradient lets phagocytes almost anywhere have a chance of picking up some food.
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